Substituent effects in cation/pi interactions and electrostatic potentials above the centers of substituted benzenes are due primarily to through-space effects of the substituents

Origins of Diastereoselectivity in the Addition of Enoxysilanes to Vinyl Diazonium Salts

The addition of enoxysilanes to vinyl diazonium ions occurs with varying levels of diastereoselectivity. To understand the origins of the stereoselectivity, we studied these transformations using density functional theory (DFT) calculations. The selectivity stems from a stabilizing cation-π interaction that orients the nucleophile and the diazonium ion.

Contribution of Electrostatic CH3-π Interactions to Recognition of Histone Asymmetric Dimethylarginine by the SPIN1 Triple Tudor Domain

Methylation of arginine (Arg) residues on histones creates a new binding epitope, enabling recognition by aromatic cage binding pockets in Tudor domains; these protein-protein interactions (PPIs) govern gene expression. Despite their biological importance, the molecular details of methylated Arg recognition are poorly understood. While the desolvation, hydrogen bonding, and guanidinium stacking of methylated Arg have been explored in model systems and proposed to contribute to binding, direct interactions between the methyl groups and the aromatic residues in the binding pocket have not previously been investigated. Herein, we mechanistically study the CH3-π interactions between the SPIN1 triple Tudor domain and histone asymmetric dimethylarginine. We find that these CH3-π interactions are electrostatically tunable, exhibiting cation-π character, albeit attenuated relative to cation-π interactions with quaternary ammonium ions, offering key insight into how methylation of Arg alters its binding epitope to enable new PPIs.

Modeling the behavior of monoclonal antibodies on hydrophobic interaction chromatography resins

Monoclonal antibodies (mAbs) require a high level of purity for regulatory approval and safe administration. High-molecular weight (HMW) species are a common impurity associated with mAb therapies. Hydrophobic interaction chromatography (HIC) resins are often used to remove these HMW impurities. Determination of a suitable HIC resin can be a time and resource-intensive process. In this study, we modeled the chromatographic behavior of seven mAbs across 13 HIC resins using measurements of surface hydrophobicity, surface charge, and thermal stability for mAbs, and hydrophobicity and zeta-potential for HIC resins with high fit quality (adjusted R2 > 0.80). We identified zeta-potential as a novel key modeling parameter. When using these models to select a HIC resin for HMW clearance of a test mAb, we were able to achieve 60% HMW clearance and 89% recovery. These models can be used to expedite the downstream process development for mAbs in an industry setting.

Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands

In the last 40 years, cation-π interactions have become part of the lexicon of noncovalent forces that drive protein binding. Indeed, tetraalkylammoniums are universally bound by aromatic cages in proteins, suggesting that cation-π interactions are a privileged mechanism for binding these ligands. A prominent example is the recognition of histone trimethyllysine (Kme3) by the conserved aromatic cage of reader proteins, dictating gene expression. However, two proteins have recently been suggested as possible exceptions to the conventional understanding of tetraalkylammonium recognition. To broadly interrogate the role of cation-π interactions in protein binding interactions, we report the first large-scale comparative evaluation of reader proteins for a neutral Kme3 isostere, experimental and computational mechanistic studies, and structural analysis. We find unexpected widespread binding of readers to a neutral isostere with the first examples of readers that bind the neutral isostere more tightly than Kme3. We find that no single factor dictates the charge selectivity, demonstrating the challenge of predicting such interactions. Further, readers that bind both cationic and neutral ligands differ in mechanism: binding Kme3 via cation-π interactions and the neutral isostere through the hydrophobic effect in the same aromatic cage. This discovery explains apparently contradictory results in previous studies, challenges traditional understanding of molecular recognition of tetraalkylammoniums by aromatic cages in myriad protein-ligand interactions, and establishes a new framework for selective inhibitor design by exploiting differences in charge dependence.

Utilization of the through-space effect to design donor-acceptor systems of pyrrole, indole, isoindole, azulene and aniline

Molecular electrostatic potential (MESP) topology analysis reveals the underlying phenomenon of the through-space effect (TSE), which imparts electron donor-acceptor properties to a wide range of chemical systems, including derivatives of pyrrole, indole, isoindole, azulene, and aniline. The TSE is inherent in pyrrole owing to the strong polarization of electron density (PoED) from the formally positively charged N-center to the C3C4 bonding region. The N → C3C4 directional nature of the TSE has been effectively employed to design molecules with high electronic polarization, such as bipyrroles, polypyrroles, phenyl pyrroles, multi-pyrrolyl systems and N-doped nanographenes. In core-expanded structures, the direction of electron flow from pyrrole units towards the core leads to highly electron-rich systems, while the opposite arrangement results in highly electron-deficient systems. Similarly, the MESP analysis reveals the presence of the TSE in azulene, indole, isoindole, and aniline. Oligomeric chains of these systems are designed in such a way that the direction of electron flow is consistent across each monomer, leading to substantial electronic polarization between the first and last monomer units. Notably, these designed systems exhibit strong donor-acceptor characteristics despite the absence of explicit donor and acceptor moieties, which is supported by FMO analysis, APT charge analysis, NMR data and λmax data. Among the systems studied, the TSEs of many experimentally known systems (bipyrroles, phenyl pyrroles, hexapyrrolylbenzene, octapyrrolylnaphthalene, decapyrrolylcorannulene, polyindoles, polyazulenes, etc.) are unraveled for the first time, while numerous new systems (polypyrroles, polyisoindoles, and amino-substituted benzene polymers) are predicted to be promising materials for the creation of donor-acceptor systems. These findings demonstrate the potential of the TSE in molecular design and provide new avenues for creating functional materials.

Investigating Substituent Interactions with Cationic Catalysts

Rates of isothiourea catalyzed silylation and acylation reactions were measured for substrates with various electronic substituents at the aryl group. Through these measurements, the intermolecular interactions between cationic catalyst intermediates and different aryl groups were explored. These studies were performed to understand how changes in the catalyst structure affected electrostatic intermolecular interactions. Three different catalysts (N-methylimidazole and two isothioureas) were employed that varied in their ability to delocalize their cationic nature. The results show that more delocalization on the catalyst reduces the sensitivity to the electronics on the aryl group. Surprisingly, the isothiourea with a fused benzene ring provided additional points of interaction with groups that contained lone-pairs, significantly affecting the overall rate. This work helps explore the interactions that dominate in these types of catalytic systems, to aid in future organocatalysis development. Density functional theory (DFT) studies further confirmed isothiourea/aryl ring interaction with the alcohol substrate in the acylation process, which confirmed these hypotheses. Electron rich or lone-pair bearing functional groups stabilize the cationic catalyst core, thereby stabilizing the transition states and accelerating the reaction. It was also discovered that in one case, the formation of a stable substrate dimer was responsible for its lower reactivity.

C-H···π interactions disrupt electrostatic interactions between non-aqueous electrolytes to increase solubility

Grid-scale energy storage applications, such as redox flow batteries, rely on the solubility of redox-active organic molecules. Although redox-active pyridiniums exhibit exceptional persistence in multiple redox states at low potentials (desirable properties for energy storage applications), their solubility in non-aqueous media remains low, and few practical molecular design strategies exist to improve solubility. Here we convey the extent to which discrete, attractive interactions between C-H groups and π electrons of an aromatic ring (C-H···π interactions) can describe the solubility of N-substituted pyridinium salts in a non-aqueous solvent. We find a direct correlation between the number of C-H···π interactions for each pyridinium salt and its solubility in acetonitrile. The correlation presented in this work highlights a consequence of disrupting strong electrostatic interactions with weak dispersion interactions, showing how minimal structural change can dramatically impact pyridinium solubility.

Binding propensity and selectivity of cationic, anionic, and neutral guests with model hydrophobic hosts: A first principles study

Computations play a critical role in deciphering the nature of host-guest interactions both at qualitative and quantitative levels. Reliable quantum chemical computations were employed to assess the nature, binding strength, and selectivity of ionic, and neutral guests with benzenoid hosts. Optimized complex structures reveal that alkali and ammonium ions are found to be in the hydrophobic cavity, while halide ions are outside, while both complexes elicit substantial binding energy. The origin of the selectivity of host toward the guest has been traced to the interaction and deformation energies, and the nature of associated interactions is quantified using energy decomposition and the Quantum Theory of Atoms in Molecules analyses. While the larger hosts lead to loosely bound complexes, as assessed by the longer intermolecular distances, the binding strengths are proportional to the size of the host systems. The binding of cationic complexes is electrostatic or polarization driven while exchange term dominates the anionic complexes. In contrast, dispersion contribution is a key in neutral complexes and plays a pivotal role in stabilizing the polyatomic complexes.

Structural and Energetic Origin of Different Product Specificities and Activities for SETD3 and Its Mutants on the Methylation of the β-Actin H73K Peptide: Insights from a QM/MM Study

The methylation of the lysine residue can affect some fundamental biological processes, and specific biological effects of the methylations are often related to product specificity of methyltransferases. The question remains concerning how active-site structural features and dynamics control the activity as well as the number (1, 2, or 3) of methyl groups on methyl lysine products. SET domain containing protein 3 (SETD3) has been identified recently as the β-actin histidine73-N₃ methyltransferase, and also, it has a weak methylation activity on the H73K β-actin peptide for which the target H73 residue is mutated into K73. Interestingly, the K73 methylation activity of SETD3 increases significantly as a result of the N255 → A or N255 → F/W273 → A mutation, and the N255A product specificity also differs from that of wild-type. Here, we performed QM/MM molecular dynamics and potential of mean force (PMF) simulations for SETD3 and its mutants (N255A and N255F/W273A) to study how SETD3 and its mutants could have different product specificities and activities for the K73 methylation. The PMF simulations show that the barrier for the first methylation of K73 is higher compared to the barrier of the H73 methylation in SETD3. Moreover, the second methylation of K73 has been found to have a barrier from the free energy simulation that is higher by 2.2 kcal/mol compared to the barrier of the first methyl transfer to K73, agreeing with the suggestion that SETD3 is a monomethylase. For the first, second, and third methylations of K73 in the N255A mutant, the barriers obtained from the PMF simulations for transferring the second and third methyl groups are found to be lower relative to the barrier for the first methyl transfer. Thus, N255A can be considered as a trimethyl lysine methyltransferase. In addition, for the first K73 methylation, the activities from the PMF simulations follow the order of N255F/W273A > N255A > WT, in agreement with experiments. The examination of the structural and dynamic results at the active sites provides better understanding of different product specificities and activities for the K73 methylations in SETD3 and its mutants. It is demonstrated that the existence of well-balanced interactions at the active site leading to the near attack conformation is of crucial importance for the efficient methyl transfers. Moreover, the presence of potential interactions (e.g., the C-H···O and cation-π interactions) that are strengthening at the transition state can also be important. Furthermore, the activity as well as product specificity of the K73 methylation also seems to be controlled by certain active-site water molecules which may be released to provide extra space for the addition of more methyl groups on K73.

Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain

Amide-π interactions, in which an amide interacts with an aromatic group, are ubiquitous in biology, yet remain understudied relative to other noncovalent interactions. Recently, we demonstrated that an electrostatically tunable amide-π interaction is key to recognition of histone acyllysine by the AF9 YEATS domain, a reader protein which has emerged as a therapeutic target due to its dysregulation in cancer. Amide isosteres are commonly employed in drug discovery, often to prevent degradation by proteases, and have proven valuable in achieving selectivity when targeting epigenetic proteins. However, like amide-π interactions, interactions of amide isosteres with aromatic rings have not been thoroughly studied despite widespread use. Herein, we evaluate the recognition of a series of amide isosteres by the AF9 YEATS domain using genetic code expansion to evaluate the amide isostere-π interaction. We show that compared to the amide-π interaction with the native ligand, each isostere exhibits similar electrostatic tunability with an aromatic residue in the binding pocket, demonstrating that the isosteres maintain similar interactions with the aromatic residue. We identify a urea-containing ligand that binds with enhanced affinity for the AF9 YEATS domain, offering a promising starting point for inhibitor development. Furthermore, we demonstrate that carbamate and urea isosteres of crotonyllysine are resistant to enzymatic removal by SIRT1, a protein that cleaves acyl post-translational modifications, further indicating the potential of amide isosteres in YEATS domain inhibitor development. These results also provide experimental precedent for interactions of these common drug discovery moieties with aromatic rings that can inform computational methods.

Electrostatic Complementarity in Structure-Based Drug Design

Optimization of electrostatic complementarity is an important strategy in structure-based drug discovery for improving the affinity of molecules against a specific protein target. In this Miniperspective we identify examples where deliberate optimization of protein-ligand electrostatic complementarity or intramolecular electrostatic interactions gave improvements in target affinity (up to 250-fold), physicochemical properties, in vitro properties, and off-target selectivity. We also look retrospectively at a series of factor Xa inhibitors that show an almost 8000-fold range in potency that can be correlated with the calculated electrostatic potential (ESP) surfaces. Recent developments using a graph-convolutional deep neural network to rapidly generate high quality ESP surfaces have the potential to make this useful tool more accessible for a wider audience within the field of medicinal chemistry.

Systematic Variation of Both the Aromatic Cage and Dialkyllysine via GCE-SAR Reveal Mechanistic Insights in CBX5 Reader Protein Binding

Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in transcriptional regulation and disease. Optimized peptide-based chemical probes targeting methyllysine readers favor larger alkyllysine residues in place of methyllysine. However, the mechanism by which these larger substituents drive tighter binding is not well understood. This study describes the development of a two-pronged approach combining genetic code expansion (GCE) and structure-activity relationships (SAR) through systematic variation of both the aromatic binding pocket in the protein and the alkyllysine residues in the peptide to probe inhibitor recognition in the CBX5 chromodomain. We demonstrate a novel change in driving force for larger alkyllysines, which weaken cation-π interactions but increases dispersion forces, resulting in tighter binding. This GCE-SAR approach establishes discrete energetic contributions to binding from both ligand and protein, providing a powerful tool to gain mechanistic understanding of SAR trends.

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.

Coupling experiments with calculations to understand the thermodynamics evolution for the sorption of zwitterionic ciprofloxacin on oxidizing-aged pyrogenic chars in the aquatic system

Oxidized aging due to the long-term exposure can significantly alter the sorption of pyrogenic chars (i.e., biochar, BC) towards antibiotics, which determined their fates in natural environments. In this study, the sorption of ciprofloxacin (CIP) on the oxidizing-aged BCs was studied linking the experimental thermodynamics and theoretical calculations. Results revealed that Q₀ of CIP negatively correlated with their average site energies (E_m), while pore-normalized Q₀ on aged BCs were 2-6 folds higher than fresh BCs. From competitive sorption, it is proposed that the transformation of CIP^± to CIP⁺ occurred and the π⁺-π electron donor-acceptor interaction and Coulombic attraction onto the aged BCs played a critical role. These two specific interactions with CIP were thermodynamically improved when aging degree increased and favored the free energies (Δ_aG) of sorption by 2-5 kJ mol^-1. Based on the identified relationship between experimental Δ_OA-ΔG⁰ with E_a through DFT calculations, the contributions of the specific interactions to antibiotic sorption on aged BCs were quantified. This study provided an in-depth understanding of how the aging process affects the sorption of zwitterionic antibiotics on BCs and also possibilities to predict the fate of antibiotics in the presence of BCs over a long-term period.

The Neglected Nuclei

Since the nuclei in a molecule are treated as stationary, it is perhaps natural that interpretations of molecular properties and reactivity have focused primarily upon the electronic density distribution. The role of the nuclei has generally received little explicit consideration. Our objective has been to at least partially redress this imbalance in emphasis. We discuss a number of examples in which the nuclei play the determining role with respect to molecular properties and reactive behavior. It follows that conventional interpretations based solely upon electronic densities and donating or withdrawing tendencies should be made with caution.

More Than π-π-π Stacking: Contribution of Amide-π and CH-π Interactions to Crotonyllysine Binding by the AF9 YEATS Domain

Lysine crotonylation (Kcr) is a histone post-translational modification that is implicated in numerous epigenetic pathways and diseases. Recognition of Kcr by YEATS domains has been proposed to occur through intermolecular amide-π and alkene-π interactions, but little is known about the driving force of these key interactions. Herein, we probed the recognition of lysine crotonylation and acetylation by the AF9 YEATS domain through incorporation of noncanonical Phe analogs with distinct electrostatics at two positions. We found that amide-π interactions between AF9 and acyllysines are electrostatically tunable, with electron-rich rings providing more favorable interactions. This differs from trends in amide-heteroarene interactions and provides insightful information for therapeutic design. Additionally, we report for the first time that CH-π interactions at Phe28 directly contribute to AF9's recognition of acyllysines, illuminating differences among YEATS domains, as this residue is not highly conserved but has been shown to impart selectivity for specific post-translational modification.

Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase

Most terpene synthase reactions follow Markovnikov rules for formation of high-energy carbenium ion intermediates. However, there are notable exceptions. For example, pentalenene synthase (PS) undergoes an initial anti-Markovnikov cyclization reaction followed by a 1,2-hydride shift to form an intermediate humulyl cation with positive charge on the secondary carbon C9 atom of the farnesyl diphosphate substrate. The mechanism by which these enzymes stabilize and guide the regioselectivity of secondary carbocations has not heretofore been elucidated. In an effort to better understand these reactions, we grew crystals of apo-PS, soaked them with the nonreactive substrate analogue 12,13-difluorofarnesyl diphosphate, and determined the X-ray structure of the resulting complex at 2.2 Å resolution. The most striking feature of the active site structure is that C9 is perfectly positioned to make a C-H···π interaction with the side chain benzene ring of residue F76; this would enhance hyperconjugation to stabilize a developing cation at C10 and thus support the anti-Markovnikov regioselectivity of the cyclization. The benzene ring is also positioned to catalyze the migration of H to C10 and stabilize a C9 carbocation. On the opposite face of C9, further cation stabilization is possible via interactions with the main chain carbonyl of I177 and the neighboring intramolecular C6═C7 bond. Mutagenesis experiments also support a role for residue 76 in these interactions, but most interesting is the F76W mutant, whose crystal structure clearly shows C9 and C10 centered above the fused benzene and pyrrole rings of the indole side chain, respectively, such that a carbocation at either position could be stabilized in this complex, and two anti-Markovnikov products, pentalenene and humulene, are formed. Finally, we show that there is a rough correlation (although not absolute) of an aromatic side chain (F or Y) at position 76 in related terpene synthases from Streptomyces that catalyze similar anti-Markovnikov addition reactions.

Changes in Electron Structure of the Triple Bond in Substituted Acetylene and Diacetylene Derivatives

The substituent effect is usually considered by means of various Hammett-like substituent constants and is most often related to aromatic systems. Unlike this, we present results of our research on the influence of 27 substituents spanning a wide range of electronic properties, from strongly electron-withdrawing to strongly electron-donating, on the electron structure of X-substituted acetylenes and diacetylenes - thus the systems which until now have practically not been subject of any deeper studies. It is shown that the interaction through triple bond(s) is associated with a significant advantage of resonance effects and that the substituent effect transmitted by the C≡C-C≡C unit is about half of that transmitted by the C≡C unit alone. Substituent X mainly affects the closest carbon atom by means of proximity effect, hence changes of charge on this atom do not follow any substituent constants. The effect on further carbon atoms is much smaller. The presence of the C≡C-C≡C unit withdraws more charge from X than a triple bond alone, and hinders communication between X and the terminal H atom. Comparison of substituent effects to those present in X-substituted benzene derivatives shows that the electronic properties of the terminal hydrogen atom in acetylenes and diacetylenes are most similar to the electronic properties of ortho and para hydrogen atoms in X-substituted benzene derivatives.

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.

Interplay between σ Holes, Anion···H-C, and Cation-π Interactions in Dibromo[2,2]paracyclophane Complexes

Theoretical calculations were performed to investigate the interplay between σ-hole, anion-HC and cation-π interactions in the complexes of dibromo[2,2]paracyclophane (DBr[2,2]PCP) with alkali (Li⁺, Na⁺, K⁺), alkaline earth metal cations (Be²⁺, Mg²⁺, and Ca²⁺), and halogen anions (F^-, Cl^-, and Br^-) using the wave function (MP2) and density functional theory (M06-2X and B3LYP) methods with the 6-311++G(d,p) basis set. The study reveals that DBr[2,2]PCP behaves as amphoteric molecule with a predominance of basic character. It prefers to interact with hard cations and hard anions such as Be²⁺ and F^- through cation-π and anion···HC interactions, respectively. Substitution of Br by F and Cl atoms in DBr[2,2]PCP decreases slightly the interaction energies of DX[2,2]PCP-halogen complexes (X = F, Cl, and Br) by 2.0 and 0.3 kcal/mol (M06-2X), respectively. The anion-HC interactions in DBr[2,2]PCP complexes are ∼10 kcal/mol stronger (B3LYP; ∼15 kcal/mol at M06-2X and 7 kcal/mol at MP2) than the σ-hole interactions.

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger

The understanding of biomolecular recognition of posttranslationally modified histone proteins is centrally important to the histone code hypothesis. Despite extensive binding and structural studies on the readout of histones, the molecular language by which posttranslational modifications on histone proteins are read remains poorly understood. Here we report physical-organic chemistry studies on the recognition of the positively charged trimethyllysine by the electron-rich aromatic cage containing PHD3 finger of KDM5A. The aromatic character of two tryptophan residues that solely constitute the aromatic cage of KDM5A was fine-tuned by the incorporation of fluorine substituents. Our thermodynamic analyses reveal that the wild-type and fluorinated KDM5A PHD3 fingers associate equally well with trimethyllysine. This work demonstrates that the biomolecular recognition of trimethyllysine by fluorinated aromatic cages is associated with weaker cation-π interactions that are compensated by the energetically more favourable trimethyllysine-mediated release of high-energy water molecules that occupy the aromatic cage.

Cation-π Interactions in Graphene-Containing Systems for Water Treatment and Beyond

Cation-π interactions are common in nature, especially in organisms. Their profound influences in chemistry, physics, and biology have been continuously investigated since they were discovered in 1981. However, the importance of cation-π interactions in materials science, regarding carbonaceous nanomaterials, has just been realized. The interplay between cations and delocalized polarizable π electrons of graphene would bring about significant changes to the intrinsic characteristics of graphene and greatly affect the device performance based on graphene and its derivatives. Here, the cation-π interactions in graphene containing systems for water treatment applications (e.g., separation membranes, adsorbents) are highlighted. The cross-linking effects caused by cation-π interactions contribute to membrane stability and selectivity and enhanced adsorption. Their roles in dominating the performance of graphene-based structures for other specific applications are also discussed. Relevant theoretical modeling and calculations are summarized to offer an in-depth understanding of the underlying mechanisms which can help in designing more functional materials and structures. Perspectives on the potential directions that deserve effort are also presented.

An accurate single descriptor for ion-π interactions

Non-covalent interactions between ions and π systems play an important role in molecular recognition, catalysis and biology. To guide the screen and design for artificial hosts, catalysts and drug delivery, understanding the physical nature of ion-π complexes via descriptors is indispensable. However, even with multiple descriptors that contain the leading term of electrostatic and polarized interactions, the quantitative description for the binding energies (BEs) of ion-π complexes is still lacking because of the intrinsic shortcomings of the commonly used descriptors. Here, we have shown that the impartment of orbital details into the electrostatic energy (coined as OEE) makes an excellent single descriptor for BEs of not only spherical, but also multiply-shaped, ion-π systems, highlighting the importance of an accurate description of the electrostatic interactions. Our results have further demonstrated that OEEs from a low-level method could be calibrated to BEs from a high-level method, offering a powerful practical strategy for an accurate prediction of a set of ion-π interactions.

Polyphenylene-Based Solid Acid as an Efficient Catalyst for Activation and Hydration of Alkynes

Porous polymer catalysts possess the potential to combine the advantages of heterogeneous and homogeneous catalysis, namely, easy postreaction recycling and high dispersion of active sites. Here, we designed a -SO3H functionalized polyphenylene (PPhen) framework with purely sp2-hybridized carbons, which exhibited high activity in the hydration of alkynes including challenging aliphatic substrates such as 1-octyne. The superiority of the structure lies in its covalent crosslink in the xy-plane with a π-π stacking interaction between the planes, enabling simultaneously high swellability and porosity (653 m2·g-1). High acidic site density (2.12 mmol·g-1) was achieved under a mild sulfonation condition. Similar turnover frequencies (0.015 ± 0.001 min-1) were obtained regardless of acidic density and crosslink content, suggesting high accessibility for all active sites over PPhen. In addition, the substituted benzene groups can activate alkynes through a T-shape CH/π interaction, as indicated by the 8 and 16 cm-1 red shift of the alkyne C-H stretching peak for phenylacetylene and 1-octyne, respectively, in the infrared (IR) spectra. These advantages render PPhen-SO3H a promising candidate as a solid catalyst replacing the highly toxic liquid phase acids such as the mercury salt.

Thermodynamic consequences of Tyr to Trp mutations in the cation-π-mediated binding of trimethyllysine by the HP1 chromodomain

Evolution has converged on cation–π interactions for recognition of quaternary alkyl ammonium groups such as trimethyllysine (Kme3). While computational modelling indicates that Trp provides the strongest cation–π interaction of the native aromatic amino acids, there is limited corroborative data from measurements within proteins. Herein we investigate a Tyr to Trp mutation in the binding pocket of the HP1 chromodomain, a reader protein that recognizes Kme3. Binding studies demonstrate that the Trp-mediated cation–π interaction is about −5 kcal mol⁻¹ stronger, and the Y24W crystal structure shows that the mutation is not perturbing. Quantum mechanical calculations indicate that greater enthalpic binding is predominantly due to increased cation–π interactions. NMR studies indicate that differences in the unbound state of the Y24W mutation lead to enthalpy–entropy compensation. These results provide direct experimental quantification of Trp versus Tyr in a cation–π interaction and afford insight into the conservation of aromatic cage residues in Kme3 reader domains.

In this work, we experimentally validate that tryptophan provides the strongest cation–π binding interaction among aromatic amino acids and also lend insight into the importance of residue identity in trimethyllysine recognition by reader proteins.

Density functional theory study on the donating strength of donor systems in dye-sensitized solar cells

Donating strength of typically used donors in dye-sensitized solar cells.

Interfacial Aromatics Mediating Cation-π Interactions with Choline-Containing Lipids Can Contribute as Much to Peripheral Protein Affinity for Membranes as Aromatics Inserted below the Phosphates

Membrane-binding interfaces of peripheral proteins are restricted to a small part of their exposed surface, so the ability to engage in strong selective interactions with membrane lipids at various depths in the interface, both below and above the phosphates, is an advantage. Driven by their hydrophobicity, aromatic amino acids preferentially partition into membrane interfaces, often below the phosphates, yet enthalpically favorable interactions with the lipid headgroups, above the phosphate plane, are likely to further stabilize high interfacial positions. Using free-energy perturbation, we calculate the energetic cost of alanine substitution for 11 interfacial aromatic amino acids from 3 peripheral proteins. We show that the involvement in cation-π interactions with the headgroups (i) increases the ΔΔG_transfer as compared with insertion at the same depth without cation-π stabilization and (ii) can contribute at least as much as deeper insertion below the phosphates, highlighting the multiple roles of aromatics in peripheral membrane protein affinity.

Substituent Effect Transmission Power of Alkyl, Alkenyl, Alkynyl, Phenyl, Thiophenyl, and Polyacene Spacers

The transmission of substituent effect through a variety of spacers, that is to say, alkyl, alkenyl, alkynyl, phenyl, thiophenyl, and polyacene has been studied by modeling Y-G-X type molecular systems (Y: reaction center; G: spacer moiety; X: substituent) using B3LYP/6-31G(d,p) density functional theory calculations. The reaction center is always kept as a C=C double bond and the molecular electrostatic potential (MESP) minimum (V_min ) observed for this bond showed subtle variation with respect to the changes in the spacer unit and the nature of substituent. Strong linear correlations are observed between Hammett substituent constants (σ_I and σ_p ) and V_min , which recommend the aptness of V_min as an electronic descriptor to quantify the substituent effect. Since V_min offers an alternative measure of substituent effect, the correlation between V_min and σ_p has been used for assessing the transmission of substituent effect through a variety of spacer moieties. The highest transmission coefficient (γ) is always observed for smaller spacer length. Among all the spacers, alkenyl showed the highest and alkyl showed the lowest transmission power. The study recommends the use of short chains of C=C double, C≡C triple or a combination of both as spacers for the effective transmission of substituent effect to the reaction center.

Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution

Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.

Substituent effects in the so-called cationπ interaction of benzene and its boron-nitrogen doped analogues: overlooked role of σ-skeleton

Despite massive efforts to pinpoint the substituent effects in the so-called cationπ systems, no consensus has been yet reached on how substituents exercise their effects in the interaction of the aromatic molecule with the metal ion. The π-polarization (the Hunter model) and the direct local effect (the Wheeler-Houk model) are two lines of thought applied to this problem, but the justification of both approaches is based on insufficiently proven assumptions and approximations. In order to shed more light on this issue we propose a new approach which enables us to gauge directly the energetic trends resulting from the interaction of the ring with the cation. In our method we add one more partitioning level to the interacting quantum atoms (IQA) scheme and decompose the IQA interaction energies into contributions resulting from σ and π electron densities of the aromatic ring. The new approach, which is named partitioned-IQA, abbreviated as p-IQA, has been applied to complexes of derivatives of benzene or azaborine interacting with a sodium cation. The p-IQA approach reveals that in these systems both σ and π electronic moieties are polarized. Interestingly, for the majority of cases the σ-polarization outweighs the π one, contrary to the Hunter model. However, the Wheeler-Houk model is not precise, either, since the σ-polarization shows some degree of non-locality. In addition, the substituents are found to have a negligible influence on the ring orbital-overlapping capability, i.e. the covalency. Therefore, the substituent effect in the cationπ interaction is a nonlocal classical effect, indicating that neither Hunter model nor Wheeler-Houk model is able to fully describe all the aspects of the substituent effects. The p-IQA conclusions for the considered systems have been compared with the results from the functional-group SAPT (F-SAPT) method. We believe that the presented partitioning in the IQA framework will provide a deeper insight into the substituent effects in the cationπ interactions, which is beyond the σ-π atomic charge population separation.

π-Hydrogen Bonding Probes the Reactivity of Aromatic Compounds: Nitration of Substituted Benzenes

The shifts of phenol O-H stretching vibration frequencies [Δν(OH)_exp] upon π-hydrogen bonding with aromatic compounds is proposed as a spectroscopic probe of the reactivity of aromatic substrates toward electrophiles. A single infrared spectrum reflecting the Δν(OH)_exp shift for an aromatic species in a reference solvent (CCl₄ in this study) provides a good estimate of reactivity. The methodology is applied in rationalizing reactivity trends for the BF₃ catalyzed nitration by methylnitrate in nitromethane of 20 aromatic reactants, including benzene, 11 methylbenzenes, several monoalkyl benzenes, the four halobenzenes, and anisole. Literature kinetic data are employed in the analysis. Very good correlations between relative rates of nitration and Δν(OH)_exp are obtained. The approach is best applied to reactions, where the initial interactions between the reactants controls the rates. A new theoretical quantity, the shifts (with respect to benzene) of the molecular electrostatic potential at 1.5 Å over the centroid of the aromatic ring [Δ V(1.5)] is defined and shown to provide a good description of substituent effects on properties of the aromatic species. B3LYP density functional and MP2 ab initio methods combined with the 6-311++G(3df,2pd) basis set are employed in evaluating the Δ V(1.5) values.

Ligand's electronegativity controls the sense of enantioselectivity in BIFOP-X palladium-catalyzed allylic alkylations

Palladium-catalyzed allylic alkylations of Na(CH(CO₂Me)₂ with 1,3-diphenylallyl acetate, employing BIFOP-X (X = H, D, Cl, CN, N3) ligands, yield the C–C coupling product (up to 91% yield, 70% ee). A NBO effect reveals a change of stereochemistry.

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.

Fabrication of aqueous nanodispersion from natural DNA and chitosan as eminent carriers for water-insoluble bioactives

For high-valued application of natural DNA as raw materials, we prepared nanocarriers by using salmon sperm DNA and chitosan to encapsulate water-insoluble bioactives. Here, water dispersible astaxanthin/DNA/chitosan nano-aggregates (ADC-NAs) were prepared by co-assemble evaporation method. The key point for preparing well formed ADC-NAs was specifically discussed. The resultant ADC-NAs were spherical with 100-300 nm diameter measured by dynamic light scattering (DLS) and transmission electron microscopy (TEM), and their homogeneous dispersions were sufficiently stable at room temperature. One important feature of these nanocarriers is enormously high loading amount of cargo (about 40 wt%). According to the UV-Vis spectra of the nanosuspension, we deduced that astaxanthin was encapsulated as uniquely structured J-aggregates. Fourier transform infra-red (FTIR) spectroscopy proved fabrication was successfully and astaxanthin was embedding in DNA/chitosan nanocarriers. Cytotoxicity was examined in vitro using cell culture in L929 cell lines. When necessary, these nano-aggregates can be degraded by DNase I. Homogeneous dispersions of other non-charged guest molecules are also prepared by using DNA/chitosan nanocarriers. These dispersions are cheaply and easily obtainable from naturally occurring DNA and chitosan, and should be useful for versatile applications.

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.