Is polarization important in cation-pi interactions?

The Implications of Drug-Polymer Interactions on the Physical Stability of Amorphous Solid Dispersions

Amorphous solid dispersions (ASDs) are a formulation and development strategy that can be used to increase the apparent aqueous solubility of poorly water-soluble drugs. Their implementation, however, can be hindered by destabilization of the amorphous form, as the drug recrystallizes from its metastable state. Factors such as the drug-polymer solubility, miscibility, mobility, and nucleation/crystal growth rates are all known to impact the physical stability of an ASD. Non-covalent interactions (NCI) between the drug and polymer have also been widely reported to influence product shelf-life. In this review, the relationship between thermodynamic/kinetic factors and adhesive NCI is assessed. Various types of NCIs reported to stabilize ASDs are described, and their role in affecting physical stability is examined. Finally, NCIs that have not yet been widely explored in ASD formulations, but may potentially impact their physical stability are also briefly described. This review aims to stimulate further theoretical and practical exploration of various NCIs and their applications in ASD formulations in the future.

Soil amended with Algal Biochar Reduces Mobility of deicing salt contaminants in the environment: An atomistic insight

Soil-based filter media in green infrastructure buffers only a minor portion of deicing salt in surface water, allowing most of that to infiltrate into groundwater, thus negatively impacting drinking water and the aquatic ecosystem. The capacity of the filter medium to adsorb and fixate sodium (Na⁺) and chloride (Cl^-) ions has been shown to improve by biochar amendment. The extent of improvement, however, depends on the type and density of functional groups on the biochar surface. Here, we use density functional theory (DFT) and molecular dynamics (MD) simulations to show the merits of biochar grafted by nitrogenous functional groups to adsorb Cl^-. Our group has shown that such functional groups are abundant in biochar made from protein-rich algae feedstock. DFT is used to model algal biochar surface and its possible interactions with Cl^- through two possible mechanisms: direct adsorption and cation (Na⁺)-bridging. Our DFT calculations reveal strong adsorption of Cl^- to the biochar surface through hydrogen bonding and electrostatic attractions between the ions and active sites on biochar. MD results indicate the efficacy of algal biochar in delaying chloride diffusion. This study demonstrates the potential of amending soils with algal biochar as a dual-targeting strategy to sequestrate carbon and prevent deicing salt contaminants from leaching into water bodies.

Single-Molecule Force Spectroscopy Reveals Cation-π Interactions in Aqueous Media Are Highly Affected by Cation Dehydration

Cation-π interactions underlie many important processes in biology and materials science. However, experimental investigations of cation-π interactions in aqueous media remain challenging. Here, we studied the cation-π binding strength and mechanism by pulling two hydrophobic polymers with distinct cation binding properties, i.e., poly-pentafluorostyrene and polystyrene, in aqueous media using single-molecule force spectroscopy and nuclear magnetic resonance measurement. We found that the interaction strengths linearly depend on the cation concentrations, following the order of Li^{+}<NH_{4}^{+}<Na^{+}<K^{+}. The binding energies are 0.03-0.23  kJ mol^{-1} M^{-1}. This order is distinct from the strength of cation-π interactions in gas phase and may be caused by the different dehydration ability of the cations. Taken together, our method provides a unique perspective to investigate cation-π interactions under physiologically relevant conditions.

DFT calculations, structural analysis, solvent effects, and non-covalent interaction study on the para-aminosalicylic acid complex as a tuberculosis drug: AIM, NBO, and NMR analyses

In this study, the effect of non-covalent interactions on the para-aminosalicylic acid complex is explored using density functional theory (DFT) in the gas phase and the solution. Our findings exhibit that the achieved binding energies considerably change on going from the gas phase to the solution. Based on the obtained results, the absolute value of the binding energy of the complex in the polar solvents is lower than the non-polar ones while in the gas phase it is higher than the solution. The atoms in molecules (AIM) and the natural bond orbital (NBO) analyses are applied to estimate the topological properties and the charge transfer during complexation, respectively. The results indicate that the presence of the cation-π interaction increases the strength of the intramolecular hydrogen bond in the studied complex. Finally, the various electronic descriptors such as energy gap, hardness, softness, and electronic chemical potential are investigated to gain further insight into these interactions. According to the achieved results, the high energy gap of the complex in the water solvent indicates high chemical stability and low reactivity compared to the others. On the other hand, the most reactive as well as the softest complex belongs to the gas phase.

Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems

Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.

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.

Prediction of molecular interactions and physicochemical properties relevant for vasopressin V2 receptor antagonism

We have developed two ligand- and receptor-based computational approaches to study the physicochemical properties relevant to the biological activity of vasopressin V2 receptor (V2R) antagonist and eventually to predict the expected binding mode to V2R. The obtained quantitative structure activity relationship (QSAR) model showed a correlation of the antagonist activity with the hydration energy (E_H2O), the polarizability (P), and the calculated partial charge on atom N7 (q6) of the common substructure. The first two descriptors showed a positive contribution to antagonist activity, while the third one had a negative contribution. V2R was modeled and further relaxed on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocoline (POPC) membrane by molecular dynamics simulations. The receptor antagonist complexes were guessed by molecular docking, and the stability of the most relevant structures was also evaluated by molecular dynamics simulations. As a result, amino acid residues Q96, W99, F105, K116, F178, A194, F307, and M311 were identified with the probably most relevant antagonist-receptor interactions on the studied complexes. The proposed QSAR model could explain the molecular properties relevant to the antagonist activity. The contributions to the antagonist-receptor interaction appeared also in agreement with the binding mode of the complexes obtained by molecular docking and molecular dynamics. These models will be used in further studies to look for new V2R potential antagonist molecules.

Hydrodynamic slip of alkali chloride solutions in uncharged graphene nanochannels

Using non-equilibrium molecular dynamics simulations, we demonstrate the effect of concentration and alkali cation types (K⁺, Na⁺, and Li⁺) on the hydrodynamic slip of aqueous alkali chloride solutions in an uncharged graphene nanochannel. We modeled the graphene-electrolyte interactions using the potential of Williams et al. [J. Phys. Chem. Lett. 8, 703 (2017)], which uses optimized graphene-ion Lennard-Jones interaction parameters to effectively account for surface and solvent polarizability effects on the adsorption of ions in an aqueous solution to a graphene surface. In our study, the hydrodynamic slip exhibits a decreasing trend for alkali chloride solutions with increasing salt concentration. The NaCl solution shows the highest reduction in the slip length followed by KCl and LiCl solutions, and the reduction in the slip length is very much dependent on the salt type. We also compared the slip length with that calculated using a standard unoptimized interatomic potential obtained from the Lorentz-Berthelot mixing rule for the ion-carbon interactions, which is not adjusted to account for the surface and solvent polarizability at the graphene surface. In contrast to the optimized model, the slip length of alkali chloride solutions in the unoptimized model shows only a nominal change with salt concentration and is also independent of the nature of salts. Our study shows that adoption of the computationally inexpensive optimized potential of Williams et al. for the graphene-ion interactions has a significant influence on the calculation of slip lengths for electrolyte solutions in graphene-based nanofluidic devices.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

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

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

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.

Cation-π Interactions and Their Contribution to Mussel Underwater Adhesion Studied Using a Surface Forces Apparatus: A Mini-Review

Mussel underwater adhesion is a model phenomenon important for the understanding of broader biological adhesion and the development of biomimetic wet adhesives. The catechol moiety of 3,4-dihydroxyphenyl-l-alanine (DOPA) is known to be actively involved in the mechanism of mussel underwater adhesion; however, other underwater adhesion mechanisms are also crucial. The surface forces apparatus (SFA) has often been used to explore the contributions of other mechanisms to mussel underwater adhesion; e.g., recent SFA-based nanomechanical studies have revealed that cation-π interactions, one of the strongest intermolecular interactions in water, are the pivotal interactions of adhesive proteins involved in underwater mussel adhesion. This mini-review surveys recent research on cation-π interactions and their contributions to strong mussel underwater adhesion, shedding light on some biological processes and facilitating the development of biomedical adhesives.

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.

Desorption of Benzene, 1,3,5-Trifluorobenzene, and Hexafluorobenzene from a Graphene Surface: The Effect of Lateral Interactions on the Desorption Kinetics

The desorption of benzene, 1,3,5-trifluorobenzene (TFB), and hexafluorobenzene (HFB) from a graphene covered Pt(111) substrate was investigated using temperature-programmed desorption (TPD). All three species have well-resolved monolayer and second-layer desorption peaks. The desorption spectra for submonolayer coverages of benzene and HFB are consistent with first-order desorption kinetics. In contrast, the submonolayer TPD spectra for TFB align on a common leading-edge, which is indicative of zero-order desorption kinetics. The desorption behavior of the three molecules can be correlated with the strength of the quadrupole moments. Calculations (second-order Møller-Plesset perturbation and density functional theory) show that the potential minimum for coplanar TFB dimers is more than a factor of 2 greater than that for either benzene or HFB dimers. The calculations support the interpretation that benzene and HFB are less likely to form the two-dimensional islands that are needed for submonolayer zero-order desorption kinetics.

Exploiting non-covalent π interactions for catalyst design

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

Structural and energetic study of cation–π–cation interactions in proteins

Statistical and energetic analysis of cation–π–cation motifs in protein structures suggests a potential stabilizing role in the protein fold.

Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions

Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.

The Cation-π Interaction in Small-Molecule Catalysis

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

σ-Hole Bond vs π-Hole Bond: A Comparison Based on Halogen Bond

The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future.

Cation–π interactions in CREBBP bromodomain inhibition: an electrostatic model for small-molecule binding affinity and selectivity

A new model is presented to explain and predict binding affinity of aromatic and heteroaromatic ligands for the CREBBP bromodomain based on cation–π interaction strength.

Prediction of Intramolecular Polarization of Aromatic Amino Acids Using Kriging Machine Learning

Present computing power enables novel ways of modeling polarization. Here we show that the machine learning method kriging accurately captures the way the electron density of a topological atom responds to a change in the positions of the surrounding atoms. The success of this method is demonstrated on the four aromatic amino acids histidine, phenylalanine, tryptophan, and tyrosine. A new technique of varying training set sizes to vastly reduce training times while maintaining accuracy is described and applied to each amino acid. Each amino acid has its geometry distorted via normal modes of vibration over all local energy minima in the Ramachandran map. These geometries are then used to train the kriging models. Total electrostatic energies predicted by the kriging models for previously unseen geometries are compared to the true energies, yielding mean absolute errors of 2.9, 5.1, 4.2, and 2.8 kJ mol(-1) for histidine, phenylalanine, tryptophan, and tyrosine, respectively.

Modeling Induction Phenomena in Intermolecular Interactions with an Ab Initio Force Field

One possible road toward the development of a polarizable potential energy function relies on the use of distributed polarizabilities derived from the induction energy mapped around the molecule. Whereas such polarizable models are expected to reproduce the signature induction energy with an appreciable accuracy, it is far from clear whether they will perform equally well in the context of intermolecular interactions. To address this issue, while pursuing the ultimate goal of a "plug-and-play"-like approach, polarizability models determined quantum mechanically and consisting of atomic isotropic dipole plus charge-flow polarizabilities were combined with the classical, nonpolarizable Charmm force field. Performance of the models was probed in the challenging test cases of cation-π binding and the association of a divalent calcium ion with water, where induction effects are envisioned to be considerable. Since brute force comparison of the binding energies estimated from the polarizable and the classical Charmm potential energy functions is not justified, the individual electrostatic and induction contributions of the force field were confronted to the corresponding terms of a symmetry-adapted perturbation theory (SAPT) expansion carried out with the 6-311++G(d,p) basis set. While the quantum-mechanical and the molecular-mechanical electrostatic and damped induction contributions agree reasonably well, overall reproduction of the binding energies is plagued by an underestimated repulsion that underlines the necessity of de novo parametrization of the classical 6-12 form of the van der Waals potential. Based on the SAPT expansion, new Lennard-Jones parameters were optimized, which, combined with the remainder of the polarizable force field, yield an improved reproduction of the target binding energies.

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins

A large number of structurally diverse epigenetic reader proteins specifically recognize methylated lysine residues on histone proteins. Here we describe comparative thermodynamic, structural and computational studies on recognition of the positively charged natural trimethyllysine and its neutral analogues by reader proteins. This work provides experimental and theoretical evidence that reader proteins predominantly recognize trimethyllysine via a combination of favourable cation-π interactions and the release of the high-energy water molecules that occupy the aromatic cage of reader proteins on the association with the trimethyllysine side chain. These results have implications in rational drug design by specifically targeting the aromatic cage of readers of trimethyllysine.

Cation-exchanged SAPO-34 for adsorption-based hydrocarbon separations: predictions from dispersion-corrected DFT calculations

The interaction of C₂ and C₃ hydrocarbons with cation-exchanged SAPO-34 materials is studied using DFT-D calculations, permitting predictions regarding their suitability for alkene–alkane separations.