Substituent effects on aromatic stacking interactions

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.

The Persistence of Hydrogen Bonds in Pyrimidinones: From Solution to Crystal

Pyrimidinone scaffolds are present in a wide array of molecules with synthetic and pharmacological utility. The inherent properties of these compounds may be attributed to intermolecular interactions analogous to the interactions that molecules tend to establish with active sites. Pyrimidinones and their fused derivatives have garnered significant interest due to their structural features, which resemble nitrogenous bases, the foundational building blocks of DNA and RNA. Similarly, pyrimidinones are predisposed to forming N-H···O hydrogen bonds akin to nitrogenous bases. Given this context, this study explored the supramolecular features and the predisposition to form hydrogen bonds in a series of 18 substituted 4-(trihalomethyl)-2(1H)-pyrimidinones. The formation of hydrogen bonds was observed in solution via nuclear magnetic resonance (NMR) spectroscopy experiments, and subsequently confirmed in the crystalline solid state. Hence, the 18 compounds were crystallized through crystallization assays by slow solvent evaporation, followed by single-crystal X-ray diffraction (SC-XRD). The supramolecular cluster demarcation was employed to evaluate all intermolecular interactions, and all crystalline structures exhibited robust hydrogen bonds, with an average energy of approximately -21.64 kcal mol-1 (∼19% of the total stabilization energy of the supramolecular clusters), irrespective of the substituents at positions 4, 5, or 6 of the pyrimidinone core. To elucidate the nature of these hydrogen bonds, an analysis based on the quantum theory of atoms in molecules (QTAIM) revealed that the predominant intermolecular interactions are N-H···O (average of -16.55 kcal mol-1) and C-H···O (average of -6.48 kcal mol-1). Through proposing crystallization mechanisms based on molecular stabilization energy data and contact areas between molecules and employing the supramolecular cluster and retrocrystallization concepts, it was determined that altering the halogen (F/Cl) at position 4 of the pyrimidinone nucleus modifies the crystallization mechanism pathway. Notably, the hydrogen bonds present in the initial proposed steps were confirmed by 1H NMR experiments using concentration-dependent techniques.

Compatibility of polar organic chemical integrative sampler (POCIS) with compound specific isotope analysis (CSIA) of substituted chlorobenzenes

Compound specific isotope analysis (CSIA) is a powerful technique to demonstrate in situ degradation of traditional groundwater contaminants when concentrations are typically in the mg/L range. Currently, an efficient preconcentration method is lacking to expand CSIA to low aqueous concentration environmental samples. Specially for the H- and N-CSIA of heteroatom-bearing non-traditional compounds, the CSIA analytical detection limits are significantly higher than that of the C-CSIA. This work demonstrates the compatibility of polar organic chemical integrative sampler (POCIS) with C-, H-, and N-CSIA using four nitro- and amino-substituted chlorobenzenes that are common industrial feedstocks for numerous applications and are commonly detected in the environment at mg/L to μg/L range. Using lab experiments, we showed isotopic equilibrium in POCIS was achieved after 30 days with either a negligible (<0.5 ‰) or a constant shift for C (<1 ‰) and N (<2 ‰). Similar negligible (<5 ‰) or constant shift (<20 ‰) was evident for H isotope except for 3,4-dichloroaniline. The method quantification limits for the combined sorbent and membrane of one POCIS were comparable to that of the solid phase extraction (SPE) using 10 L water. Next, we demonstrated the field applicability of POCIS for C- and N-CSIA after a 60-day deployment in a pilot constructed wetland by showing <1 ‰ difference between the δ13C and δ15N obtained from POCIS and SPE. Finally, we evaluated whether the biofilm development on POCIS membrane could affect the isotope signature of the sampled compounds during field deployment. Although a diverse microbial community was identified on the membrane after a 60-day deployment, we did not observe significant isotope fractionation. This was likely due to either slower diffusion in the biofilm or microbial degradation of the sampled compounds. This work demonstrates the potential of using POCIS-CSIA as a simple, fast, and sensitive method for low-concentration contaminants, such as pesticides, pharmaceuticals, and flame-retardants.

Iron-Catalyzed Intermolecular C-H Amination Assisted by an Isolated Iron-Imido Radical Intermediate

Here we report the use of a base metal complex [(tBu pyrpyrr2 )Fe(OEt2 )] (1-OEt2 ) (tBu pyrpyrr2 2- =3,5-tBu2 -bis(pyrrolyl)pyridine) as a catalyst for intermolecular amination of Csp3 -H bonds of 9,10-dihydroanthracene (2 a) using 2,4,6-trimethyl phenyl azide (3 a) as the nitrene source. The reaction is complete within one hour at 80 °C using as low as 2 mol % 1-OEt2 with control in selectivity for single C-H amination versus double C-H amination. Catalytic C-H amination reactions can be extended to other substrates such as cyclohexadiene and xanthene derivatives and can tolerate a variety of aryl azides having methyl groups in both ortho positions. Under stoichiometric conditions the imido radical species [(tBu pyrpyrr2 )Fe{=N(2,6-Me2 -4-tBu-C6 H2 )] (1-imido) can be isolated in 56 % yield, and spectroscopic, magnetometric, and computational studies confirmed it to be an S = 1 FeIV complex. Complex 1-imido reacts with 2 a to produce the ferrous aniline adduct [(tBu pyrpyrr2 )Fe{NH(2,6-Me2 -4-tBu-C6 H2 )(C14 H11 )}] (1-aniline) in 45 % yield. Lastly, it was found that complexes 1-imido and 1-aniline are both competent intermediates in catalytic intermolecular C-H amination.

Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6

Heteroaromatic stacking interactions are important in drug binding, supramolecular chemistry, and materials science, making protein-ligand model systems of these interactions of considerable interest. Here we studied 30 congeneric ligands that each present a distinct heteroarene for stacking between tyrosine residues at the dimer interface of procaspase-6. Complex X-ray crystal structures of 10 analogs showed that stacking geometries were well conserved, while high-accuracy computations showed that heteroarene stacking energy was well correlated with predicted overall ligand binding energies. Empirically determined KD values in this system thus provide a useful measure of heteroarene stacking with tyrosine. Stacking energies are discussed in the context of torsional strain, the number and positioning of heteroatoms, tautomeric state, and coaxial orientation of heteroarene in the stack. Overall, this study provides an extensive data set of empirical and high-level computed binding energies in a versatile new protein-ligand system amenable to studies of other intermolecular interactions.

Substituent effects on aromatic interactions in water

Molecular recognition in water involves contributions due to polar functional group interactions, partial desolvation of polar and non-polar surfaces and changes in conformational flexibility, presenting a challenge for rational design and interpretation of supramolecular behaviour. Conformationally well-defined supramolecular complexes that can be studied in both water and non-polar solvents provide a platform for disentangling these contributions. Here 1 : 1 complexes formed between four different calix[4]pyrrole receptors and thirteen different pyridine N-oxide guests have been used to dissect the factors that govern substituent effects on aromatic interactions in water. H-bonding interactions between the receptor pyrrole donors and the guest N-oxide acceptor at one end of the complex lock the geometrical arrangement of a cluster of aromatic interactions at the other end of the complex, so that a phenyl group on the guest makes two edge-to-face and two stacking interactions with the four aromatic side-walls of the receptor. The thermodynamic contribution of these aromatic interactions to the overall stability of the complex was quantified by chemical double mutant cycles using isothermal titration calorimetry and ¹H NMR competition experiments. Aromatic interactions between the receptor and a phenyl group on the guest stabilise the complex by a factor of 1000, and addition of substituents to the guest phenyl group further stabilises the complex by an additional factor of up to 1000. When a nitro substituent is present on the guest phenyl group, the complex has a sub-picomolar dissociation constant (370 fM). The remarkable substituent effects observed in water for these complexes can be rationalised by comparison with the magnitude of the corresponding substituent effects measured in chloroform. In chloroform, the double mutant cycle free energy measurements of the aromatic interactions correlate well with the substituent Hammett parameters. Electron-withdrawing substituents increase the strength of the interactions by a factor of up to 20, highlighting the role of electrostatics in stabilising both the edge-to-face and stacking interactions. The enhanced substituent effects observed in water are due to entropic contributions associated with the desolvation of hydrophobic surfaces on the substituents. The flexible alkyl chains that line the open end of the binding site assist the desolvation of the non-polar π-surfaces of polar substituents, like nitro, but at the same time allow water to interact with the polar H-bond acceptor sites on the substituent. This flexibility allows polar substituents to maximise non-polar interactions with the receptor and polar interactions with the solvent, leading to remarkably high binding affinities.

The surface site interaction point approach to non-covalent interactions

The functional properties of molecular systems are generally determined by the sum of many weak non-covalent interactions, and therefore methods for predicting the relative magnitudes of these interactions is fundamental to understanding the relationship between function and structure in chemistry, biology and materials science. This review focuses on the Surface Site Interaction Point (SSIP) approach which describes molecules as a set of points that capture the properties of all possible non-covalent interactions that the molecule might make with another molecule. The first half of the review focuses on the empirical non-covalent interaction parameters, α and β, and provides simple rules of thumb to estimate free energy changes for interactions between different types of functional group. These parameters have been used to have been used to establish a quantitative understanding of the role of solvent in solution phase equilibria, and to describe non-covalent interactions at the interface between macroscopic surfaces as well as in the solid state. The second half of the review focuses on a computational approach for obtaining SSIPs and applications in multi-component systems where many different interactions compete. Ab initio calculation of the Molecular Electrostatic Potential (MEP) surface is used to derive an SSIP description of a molecule, where each SSIP is assigned a value equivalent to the corresponding empirical parameter, α or β. By considering the free energies of all possible pairing interactions between all SSIPs in a molecular ensemble, it is possible to calculate the speciation of all intermolecular interactions and hence predict thermodynamic properties using the SSIMPLE algorithm. SSIPs have been used to describe both the solution phase and the solid state and provide accurate predictions of partition coefficients, solvent effects on association constants for formation of intermolecular complexes, and the probability of cocrystal formation. SSIPs represent a simple and intuitive tool for describing the relationship between chemical structure and non-covalent interactions with sufficient accuracy to understand and predict the properties of complex molecular ensembles without the need for computationally expensive simulations.

Using Macrocyclic G-Quadruplex Ligands to Decipher the Interactions Between Small Molecules and G-Quadruplex DNA

This study aims to deepen the knowledge of the current state of rational G4-ligand design through the design and synthesis of a novel set of compounds based on indoles, quinolines, and benzofurans and their comparisons with well-known G4-ligands. This resulted in novel synthetic methods and G4-ligands that bind and stabilize G4 DNA with high selectivity. Furthermore, the study corroborates previous studies on the design of G4-ligands and adds deeper explanations to why a) macrocycles offer advantages in terms of G4-binding and -selectivity, b) molecular pre-organization is of key importance in the development of strong novel binders, c) an electron-deficient aromatic core is essential to engage in strong arene-arene interactions with the G4-surface, and d) aliphatic amines can strengthen interactions indirectly through changing the arene electrostatic nature of the compound. Finally, fundamental physicochemical properties of selected G4-binders are evaluated, underscoring the complexity of aligning the properties required for efficient G4 binding and stabilization with feasible pharmacokinetic properties.

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.

Effect of Hydrogen Bonds and π...π-interactions on the Crystallization of Phenyl-perfluorophenyl Amides: Understanding the Self-organization of a Cocrystal

A series of N-arylbenzamides containing amide group and phenyl−perfluorinated rings were used as the smallest molecules to investigate the direct influence of hydrogen bond and aromatic donor-acceptor complementarity in the...

Augmented Self-Association by Electrostatic Forces in Thienopyrrole-Fused Thiadiazoles that Contain an Ester instead of an Ether Linker

During the self-assembly of π-conjugated molecules, linkers and substituents can potentially add supportive noncovalent intermolecular interactions to π-stacking interactions. Here, we report the self-assembly behavior of thienopyrrole-fused thiadiazole (TPT) fluorescent dyes that possess ester or ether linkers and dodecyloxy side chains in solution and the condensed phase. A comparison of the self-association behavior of the ester- and ether-bridged compounds in solution using detailed UV-vis, fluorescence, and NMR spectroscopic studies revealed that the subtle replacement of the ether linkers by ester linkers leads to a distinct increase in the association constant (ca. 3-4 fold) and the enthalpic contribution (ca. 3 kcal mol-1). Theoretical calculations suggest that the ester linkers, which are in close proximity to one another due to the π-stacking interactions, induce attractive electrostatic forces and augment self-association. The self-assembly of TPT dyes into well-defined 1D clusters with high aspect ratios was observed, and their morphologies and crystallinity were investigated using SEM and X-ray diffraction analyses. TPTs with ester linkers exhibit a columnar liquid crystalline mesophase in the condensed phase.

Stimuli-responsive temporary adhesives: enabling debonding on demand through strategic molecular design

Stimuli-responsive temporary adhesives constitute a rapidly developing class of materials defined by the modulation of adhesion upon exposure to an external stimulus or stimuli. Engineering these materials to shift between two characteristic properties, strong adhesion and facile debonding, can be achieved through design strategies that target molecular functionalities. This perspective reviews the recent design and development of these materials, with a focus on the different stimuli that may initiate debonding. These stimuli include UV light, thermal energy, chemical triggers, and other potential triggers, such as mechanical force, sublimation, electromagnetism. The conclusion discusses the fundamental value of systematic investigations of the structure-property relationships within these materials and opportunities for unlocking novel functionalities in future versions of adhesives.

Dissection of the Polar and Non-Polar Contributions to Aromatic Stacking Interactions in Solution

Aromatic stacking interactions have been a matter of study and debate due to their crucial role in chemical and biological systems. The strong dependence on orientation and solvent together with the relatively small interaction energies have made evaluation and rationalization a challenge for experimental and theoretical chemists. We have used a supramolecular cage formed by two tris(pyridylmethyl)amines units to build chemical Double Mutant Cycles (DMC) for the experimental measurement of the free energies of π-stacking interactions. Extrapolating the substituent effects to remove the contribution due to electrostatic interactions reveals that there is a substantial contribution to the measured stacking interaction energies which is due to non-polar interactions (-3 to -6 kJ mol-1 ). The perfectly flat nature of the surface of an aromatic ring gives π-stacking an inherent advantage over non-polar interactions with alkyl groups and accounts for the wide-spread prevalence of stacking interactions in Nature.

Self-Immolative System for Disclosure of Reactive Electrophilic Alkylating Agents: Understanding the Role of the Reporter Group

The development of stable, efficient chemoselective self-immolative systems, for use in applications such as sensors, requires the optimization of the reactivity and degradation characteristics of the self-immolative unit. In this paper, we describe the effect that the structure of the reporter group has upon the self-immolative efficacy of a prototype system designed for the disclosure of electrophilic alkylating agents. The amine of the reporter group (a nitroaniline unit) was a constituent part of a carbamate that functioned as the self-immolative unit. The number and position of substituents on the nitroaniline unit were found to play a key role in the rate of self-immolative degradation and release of the reporter group. The position of the nitro substituent (meta- vs para-) and the methyl groups in the ortho-position relative to the carbamate exhibited an influence on the rate of elimination and stability of the self-immolative system. The ortho-methyl substituents imparted a twist on the N–C (aromatic) bond leading to increased resonance of the amine nitrogen’s lone pair into the carbonyl moiety and a decrease of the leaving character of the carbamate group; concomitantly, this may also make it a less electron-withdrawing group and lead to less acidification of the eliminated β-hydrogen.

Bandgap Modulation in Zr-Based Metal-Organic Frameworks by Mixed-Linker Approach

Metal-organic frameworks (MOFs) have been a promising material for many applications, e.g., photocatalysis, luminescence-based sensing, optoelectronics, and electrochemical devices, due to their tunable electronic properties through linker functionalization. In this work, we investigate the effect of mixed organic linkers on the bandgap modulation of polymorphic zirconium-based MOFs, UiO-66 and MIL-140A using density functional theory (DFT) calculations. We show that the electronic properties of both MOFs are in contrast to Vegard's law for semiconductors, that is, mixed-linker systems exhibit bandgaps not intermediate within the range of single-linker systems. Calculations of the total and partial density of states revealed the formation of mid-gap states in mixed-linker MOFs, causing the bandgap reduction. Interestingly, although both MOFs have similar composition, the effect is more significant in MIL-140A than in UiO-66. This is due to the presence of π-π stacking interactions in MIL-140A, which does not occur in UiO-66. The simulation results reveal a direct relationship between the strength of π-π interactions and the bandgap. This illustrates that distinct structural features, particularly the orientation of organic linkers can give rise to different consequences in bandgap modulation. Moreover, this computational work highlights the possibility to engineer the electronic properties of MOFs through a mixed-linker approach.

Dually cross-linked single networks: structures and applications

Cross-linked polymers have attracted an immense attention over the years, however, there are many flaws of these systems, e.g. softness and brittleness; such materials possess non-adjustable properties and cannot recover from damage and thus are limited in their practical applications. Supramolecular chemistry offers a variety of dynamic interactions that when integrated into polymeric gels endow the systems with reversibility and responsiveness to external stimuli. A combination of different cross-links in a single gel could be the key to tackle these drawbacks, since covalent or chemical cross-linking serve to maintain the permanent shape of the material and to improve overall mechanical performance, whereas non-covalent cross-links impart dynamicity, reversibility, stimuli-responsiveness and often toughness to the material. In the present review we sought to give a comprehensive overview of the progress in design strategies of different types of dually cross-linked single gels made by researchers over the past decade as well as the successful implementations of these advances in many demanding fields where versatile multifunctional materials are required, such as tissue engineering, drug delivery, self-healing and adhesive systems, sensors as well as shape memory materials and actuators.

Do Sulfonamides Interact with Aromatic Rings?

Aromatic rings form energetically favorable interactions with many polar groups in chemical and biological systems. Recent molecular studies have shown that sulfonamides can chelate metal ions and form hydrogen bonds, however, it is presently not established whether the polar sulfonamide functionality also interacts with aromatic rings. Here, synthetic, spectroscopic, structural, and quantum chemical analyses on 2,6-diarylbenzenesulfonamides are reported, in which two flanking aromatic rings are positioned close to the central sulfonamide moiety. Fine-tuning the aromatic character by substituents on the flanking rings leads to linear trends in acidity and proton affinity of sulfonamides. This physical-organic chemistry study demonstrates that aromatic rings have a capacity to stabilize sulfonamides via through-space NH-π interactions. These results have implications in rational drug design targeting electron-rich aromatic rings in proteins.

Donor/acceptor substituted dithiafulvenes and tetrathiafulvalene vinylogues: electronic absorption, crystallographic, and computational analyses

The structural, electronic, and crystallographic properties of nitrophenyl and methoxyphenyl-substituted dithiafulvenes and tetrathiafulvalene vinylogues were systematically investigated by experimental and computational approaches.

N-Arylimide Molecular Balances: A Comprehensive Platform for Studying Aromatic Interactions in Solution

Noncovalent interactions of aromatic surfaces play a key role in many biological processes and in determining the properties and utility of synthetic materials, sensors, and catalysts. However, the study of aromatic interactions has been challenging because these interactions are usually very weak and their trends are modulated by many factors such as structural, electronic, steric, and solvent effects. Recently, N-arylimide molecular balances have emerged as highly versatile and effective platforms for studying aromatic interactions in solution. These molecular balances can accurately measure weak noncovalent interactions in solution via their influence on the folded-unfolded conformational equilibrium. The structure (i.e., size, shape, π-conjugation, and substitution) and nature (i.e., element, charge, and polarity) of the π-surfaces and interacting groups can be readily varied, enabling the study of a wide range of aromatic interactions. These include aromatic stacking, heterocyclic aromatic stacking, and alkyl-π, chalcogen-π, silver-π, halogen-π, substituent-π, and solvent-π interactions. The ability to measure a diverse array of aromatic interactions within a single model system provides a unique perspective and insights as the interaction energies, stability trends, and solvent effects for different types of interactions can be directly compared. Some broad conclusions that have emerged from this comprehensive analysis include: (1) The strongest aromatic interactions involve groups with positive charges such as pyridinium and metal ions which interact with the electrostatically negative π-face of the aromatic surface via cation-π or metal-π interactions. Attractive electrostatic interactions can also form between aromatic surfaces and groups with partial positive charges. (2) Electrostatic interactions involving aromatic surfaces can be switched from repulsive to attractive using electron-withdrawing substituents or heterocycles. These electrostatic trends appear to span many types of aromatic interactions involving a polar group interacting with a π-surface such as halogen-π, chalcogen-π, and carbonyl-π. (3) Nonpolar groups form weak but measurable stabilizing interactions with aromatic surfaces in organic solvents due to favorable dispersion and/or solvophobic effects. A good predictor of the interaction strength is provided by the change in solvent-accessible surface area. (4) Solvent effects modulate the aromatic interactions in the forms of solvophobic effects and competitive solvation, which can be modeled using solvent cohesion density and specific solvent-solute interactions.

New insights into prediction of weak π-π complex association through proton-nuclear magnetic resonance analysis

For analysis of weak π–π complexes proton-nuclear magnetic resonance (proton-NMR) simultaneously provides information of stacking configurations and association constants \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\left( K \right)$$\end{document}K However, an apparent issue for this approach is inconsistent/impossible constant estimation which often leads to unreasonable interpretation for π–π complexation. Whether or not this proton-dependent constant variation could be attributed to simple experimental uncertainties or to more sophisticated additional unspecific shielding effects (AUS effects) was addressed by means of hypothesis tests using a robust bootstrap technique in this report. Our analysis shows the significance of AUS effects on such variation in constant estimation. A following study using numeric simulation further reveals the variation patterns induced by AUS effects and concludes that the largest \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$K$$\end{document}K among the obtained \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$K$$\end{document}K estimates of a complex is considered as the best estimate of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$K$$\end{document}K due to minimum deviation from the true value of K and the multiple \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$K$$\end{document}K estimates of a π–π complex could provide preferable inferences for complex geometries.

Multicomponent and multicatalytic asymmetric synthesis of furo[2,3-b]pyrrole derivatives: further insights into the mode of action of chiral phosphoric acid catalysts

Multicomponent and multicatalytic reactions are those processes that try to imitate the way the enzymatic machinery transforms simple building blocks into complex products. The development of asymmetric versions of these reactions is a step forward in our dream of mirroring the exquisite selectivity of biological processes. In this context, the present work describes a new reaction for the asymmetric synthesis of furo[2,3-b]pyrrole derivatives from simple 3-butynamines, glyoxylic acid and anilines in the presence of a dual catalytic system, formed from a gold complex and a chiral phosphoric acid. Computations, aimed to understand the exceptional performance of 9-anthracenyl-substituted BINOL-derived phosphoric acid catalyst, suggest a fundamental role of non-covalent interactions being established between the catalyst and the reagents for the outcome of the multicomponent process. The linear geometry of the anthracenyl substituent along with the presence of an electron-withdrawing group in the aniline and an aromatic substituent in the 3-butynamine derivative seem to be key structural factors to explain the experimental results and, particularly, the high stereoselectivity.

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.

A Discrete Dichloride Tetrahydrate Trapped by a Cyclopropenium Cation: Structure and Spectroscopic Properties

A discrete dichloride tetrahydrate cluster, [Cl₂ (H₂ O)₄ ]^2- , was obtained as a salt of the bis(diphenylamino)diethylamino cyclopropenium cation [C₃ (NPh₂ )₂ (NEt₂ )]⁺ and characterized by single-crystal X-ray diffraction and infrared spectroscopy. This chloride-chloride ion-pair cluster consists of a [Cl₂ (H₂ O)₂ ]^2- square with opposite edges bridged by water molecules to give a chair-like structure of the non-hydrogen atoms. The solid-state structure is essentially the same as the calculated gas-phase structure. Infrared spectra were also collected on the deuterium analogue [Cl₂ (D₂ O)₄ ]^2- . Computational studies were carried out on gas-phase [Cl₂ (H₂ O)₄ ]^2- to confirm the infrared band assignments in the solid state. The structure and infrared spectrum are consistent with the discrete nature of the cluster.

Measurement of Solvation Ability of Solvents by Porphyrin-Based Solvation/Desolvation Indicators

A new solvent scale, solvation ability (SA), was developed to arrange solvents in the order of their SA for large π-conjugated compounds. The SA of a solvent was determined in a binary solvent system of an assessed solvent and a standard "good" solvent (GS) or "poor" solvent (PS), chloroform or methylcyclohexane, respectively, in the presence of two types of solvation/desolvation indicators, 1Zn₂ and 2Zn₂ . The latter comprises bis(imidazolylporphyrinatozinc) linked via a 1,3-butadiynylene moiety having linear alkyl and hydrophilic side chains, respectively. GSs and PSs give extended (E-) and stacked (S-) supramolecular polymers of the indicators, respectively. SA values are defined as vol % of the standard solvent added to an assessed solvent to give the balance point where comparable amounts of E- and S-polymers of the indicators coexist. GSs and PSs have positive and negative signs, respectively. In this study, the SA of 25 solvents was determined. The SA values with indicator 1Zn₂ were as follows: ethyl acetate (-81), hexane (-66), toluene (-50), cyclohexane (-47), CCl₄ (-25), chloroform (50), and nitrobenzene (79).

Insights into the inhibitory mechanism and molecular interaction of novel alkaloids from Beilschmiedia glabra with lipoxygenase and acetylcholinesterase

In this study, the mechanism underlying acetylcholinesterase (AChE) and 5-lipoxygenase (LOX) inhibition by two novel alkaloids, beilschglabrine A and beilschglabrine B, as well as their interaction footprints on the binding pockets were investigated. The results showed that beilschglabrine A and beilschglabrine B inhibit both AChE and LOX in a competitive manner by binding to their active sites thereby interfering with substrate access. The interaction of the alkaloids with the enzymes was favorable and stable with low binding energy values which correlate well with their IC[Formula: see text]. The depicted molecular interaction, structure-energetic pattern and binding conformations confirmed that beilschglabrine A is more potent than beilschglabrine B. The differences in the binding pose and potency of the alkaloids is occasioned by an extra methyl moiety on beilschglabrine B. The chemical scaffold of the alkaloids respected Lipinski’s rule of five and may be relevant in the development of new anti-inflammatory and anti-neurodegenerative disease drugs acting via AChE and LOX inhibition.

Sorption and Desorption Mechanisms of Cationic and Zwitterionic Per- and Polyfluoroalkyl Substances in Natural Soils: Thermodynamics and Hysteresis

Sorption linearity and reversibility are implicit in models for the fate and transport of per- and polyfluoroalkyl substances (PFAS). In this study, however, we found that the sorption of cationic and zwitterionic PFAS in natural soils was highly nonlinear. The nonlinearity was so severe that it led to a variation in the coefficient of sorption by several orders of magnitude over the experimental concentration range. This implies a considerable increase in sorption as concentration falls in the natural environment. Sorption of cationic PFAS correlated strongly with the soil organic matter (SOM) content and was reversible in all soils. Sorption of zwitterionic PFAS, on the other hand, displayed concentration-dependent hysteresis in soils with a low SOM content. The irreversibility, which was associated with neither SOM, pore deformation, nor surface complexation, was likely caused by the entrapment of molecules in porous structures within inorganic components of soil aggregates. Furthermore, electrostatic interactions with negatively charged soil constituents and the hydrophobic effect were found to be major sorption driving forces for cationic/zwitterionic PFAS at low and high concentrations, respectively. The maximum electrostatic potential of PFAS ions, computed using density functional theory, was found to be a useful predictor of the sorption of ionic PFAS species.

A conserved and buried edge-to-face aromatic interaction in small ubiquitin-like modifier (SUMO) has a role in SUMO stability and function

Aromatic amino acids buried at a protein's core are often involved in mutual paired interactions. Ab initio energy calculations have highlighted that the conformational orientations and the effects of substitutions are important for stable aromatic interactions among aromatic rings, but studies in the context of a protein's fold and function are elusive. Small ubiquitin-like modifier (SUMO) is a common post-translational modifier that affects diverse cellular processes. Here, we report that a highly conserved aromatic triad of three amino acids, Phe36-Tyr51-Phe64, is a unique SUMO signature that is absent in other ubiquitin-like homologous folds. We found that a specific edge-to-face conformation between the Tyr51-Phe64 pair of interacting aromatics is vital to the fold and stability of SUMO. Moreover, the noncovalent binding of SUMO-interacting motif (SIM) at the SUMO surface was critically dependent on the paired aromatic interactions buried at the core. NMR structural studies revealed that perturbation of the Tyr51-Phe64 conformation disrupts several long-range tertiary contacts in SUMO, leading to a heterogeneous and dynamic protein with attenuated SUMOylation both in vitro and in cells. A subtle perturbation of the edge-to-face conformation by a Tyr to Phe substitution significantly decreased stability, SUMO/SIM affinity, and the rate of SUMOylation. Our results highlight that absolute co-conservation of specific aromatic pairs inside the SUMO protein core has a role in its stability and function.

Membranes with Functionalized Nanopores for Aromaticity-Based Separation of Small Molecules

Membranes that can separate molecules of similar size based on chemical features could transform chemical manufacturing. We demonstrate membranes with functional, 1-3 nm pores prepared using a simple and scalable approach: coating a porous support with random copolymer micelles in alcohol, followed by precipitation in water and functionalization of pore surfaces. This approach was used to prepare membranes that can separate two hormones of similar size and charge, differentiated by aromaticity, mediated through π-π interactions between the aromatic solute and pore walls functionalized with phenol groups. The aromatic molecule permeates more slowly in single-solute experiments. In competitive diffusion experiments, however, it permeates 7.1 times faster than its nonaromatic analogue. This approach can be used to manufacture membranes for complex separations based on various intermolecular interactions.

Hetero-association models of non-covalent molecular complexation

The present review discusses the current state-of-the-art in building models enabling the description of non-covalent equilibrium complexation of different types of molecules in solution, which results in the formation of supramolecular structures different in length and composition (hetero-association or supramolecular multicomponent co-polymerisation). The description is focused on standard physical and chemical quantities such as experimental observables and equilibrium parameters of interaction (equilibrium constants and concentrations). The major partial cases of the hetero-association models, such as finite and indefinite isodesmic and cooperative complexations, and Benesi-Hildebrand and Langmuir adsorption models are considered. Future challenges in the development of the hetero-association models are provided.

Supramolecular cage encapsulation as a versatile tool for the experimental quantification of aromatic stacking interactions

The widespread presence of aromatic stacking interactions in chemical and biological systems, combined with their relatively small energetic contribution, have led to a plethora of theoretical and experimental studies for their quantification and rationalization. Typically, π-π aromatic interactions are studied as a function of substituents to gather information about the interaction mechanism. While experiments suggest that aromatic interactions are dominated by local electrostatic contacts between π-electron density and CH groups, theoretical work has raised the possibility that direct electrostatic interactions between local dipoles of the substituents may play a role. We describe a supramolecular cage that binds two aromatic carboxylates in a stacked geometry such that the aromatic substituents are remote in space. Chemical Double Mutant Cycles (DMCs) were used to measure fifteen different aromatic stacking interactions as a function of substituent (NMe2, OMe, Me, Cl and NO2). When both aromatic rings have electron-withdrawing nitro substituents, the interaction is attractive (-2.8 kJ mol-1) due to reduced π-electron repulsion. When both aromatic rings have electron-donating di-methylamino substituents, the interaction is repulsive (+2.0 kJ mol-1) due to increased π-electron repulsion. The results show that aromatic stacking interactions are dominated by short range electrostatic contacts rather than substituent dipole interactions.

Study of through-space substituent–π interactions using N-phenylimide molecular balances

Substituent–π interactions associated with aromatic stacking interactions were experimentally measured using a small N-phenylimide molecular balance model system.

Ring-opening supramolecular polymerization controlled by orthogonal non-covalent interactions

The π–π interaction has been successfully utilized to orthogonally regulate the supramolecular polymerization driven by quadruple hydrogen bonding.

Charge transfer complexes as colour changing and disappearing–reappearing colour materials

Charge transfer complexes, made of suitably chosen electron-rich and electron-deficient components, can perform as vanishing colour, disappearing–reappearing colour and colour changing materials.

Changes in macrocyclic aromaticity and formation of a charge-separated state by complexation of expanded porphyrin and C60

Significant changes of macrocyclic aromaticity in expanded porphyrins through C60 complexation were studied by ¹H NMR spectroscopy and nucleus-independent chemical shift calculations.

Stacking Principles on π- and Lamellar Stacking for Organic Semiconductors Evaluated by Energy Decomposition Analysis

Two stacking manners, that is, π- and lamellar stacking, are generally found for organic semiconductors, in which the π-stacking occurs between conjugated groups and the lamellar stacking refers to the separation of the conjugated and aliphatic moieties. The stacking principles are yet not well-defined. In this work, extended transition state-natural orbitals for chemical valence (ETS-NOCV), an energy decomposition analysis, is utilized to examine the π- and lamellar stacking for a series of naphthalenetetracarboxylic diimide (R-NDI) crystals. The crucial role of dispersion is validated. The perception that π-stacking is merely determined by the conjugated moiety is challenged. The stacking principles are associated with the closest packing model. Nanoscopic phase separation of conjugated and aliphatic moieties and the formation of lamellar and herringbone motifs in the R-NDIs can thus be clarified. Moreover, the interactions between NDI and the alkyl chain are investigated, revealing that the interactions can be significant, being contradictory to the conventional point of view. Along with R-NDIs, additional organic crystals consisting of various conjugated functionalities and substituents are also investigated by ETS-NOCV. The sampling scope is up to 108 conjugated molecules. The dominant role of dispersion force irrespective of the variation in the conjugated moieties and substituents is further confirmed. It is envisaged that the established principles are applicable to other organic semiconductors. The perspective toward the π- and lamellar stacking might be modified, paving the way for ultimate morphological control.

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.

Borane-Induced Dimerization of Arylallenes

A series of arylallenes react with HB(C₆ F₅ )₂ in a 2:1 molar ratio to give the tail-to-tail 1,6-diaryl-2-boryl-hexa-1,5-diene coupling products. The reaction of the phenylallene substrate with HB(C₆ F₅ )₂ was shown to initially give the 2-boryl-3,4-diphenyl-1,5-hexadiene head-to-head coupling product which then rearranged, by a thermally induced Cope rearrangement, into the final product.

Size-dependent rate acceleration in the silylation of secondary alcohols: the bigger the faster

Relative rates for the reaction of secondary alcohols carrying large aromatic moieties with silyl chlorides carrying equally large substituents have been determined in organic solvents. Introducing thoroughly matching pairs of big dispersion energy donor (DED) groups enhanced rate constants up to four times, notably depending on the hydrogen bond donor ability of the solvent. A linear correlation between computed dispersion energy contributions to the stability of the silyl ether products and experimental relative rate constants was found. These results indicate a cooperation between solvophobic effects and DED-groups in the kinetic control of silylation reactions.

Construction of supramolecular hydrogels using photo-generated nitric oxide radicals

Photo-generated nitric oxide radicals (NO˙) derived from sodium nitroprusside dihydrate (SNP) are employed for the construction of supramolecular hydrogels based on an amino acid derivative precursor, N-fluorenylmethyloxycarbonyl tyrosine phosphate (FYP), which through dephosphorylation produces the gelator, N-fluorenylmethyloxycarbonyl tyrosine (FY). Self-assembly of the amphiphilic gelator yields high-aspect ratio nanofilaments that entangle to form self-supporting, viscoelastic hydrogels. The presence of photolyzed SNP yields periodically twisted nanofilaments with opposite chirality to filaments formed through conventional hydrogelation routes.