On the Nature of σ-σ, σ-π, and π-π Stacking in Extended Systems

Synthesis, structural, multitargeted molecular docking analysis of anti-cancer, anti-tubercular, DNA interactions of benzotriazole based macrocyclic ligand

Biologically important macromolecule 1, 1', 3, 3' Bis - [2,3,5,6-Tetramethyl-p-phenylenebis(methylene)] dibenzotriazlinium dibromide hydrate (BTD) was synthesized and characterized using FT-IR, NMR and single-crystal XRD (SCXRD). SCXRD revealed that the compound was crystallized as a monoclinic system and associated through weak intermolecular interactions like H-bonding and π- π stacking interactions. These weak intermolecular interactions in BTD were studied using Crystal Explorer and Gaussian. The calculated energies for the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) showed the stability and reactivity of the title compound. Molecular electrostatic potential (MEP) surface analysis was used to investigate the crystal's nucleophilic and electrophilic reactive sites. The molecular shape and intermolecular interactions in the crystal structure were determined using Hirshfeld surface analysis and fingerprint plots. Anticancer, anti-bacterial and DNA binding ability of BTD were investigated by experimental and theoretical techniques. The obtained results suggest that BTD possesses better anti-cancer, anti-bacterial and DNA binding abilities. The mode of action of antibiotic and anticancer approach was discussed. This provides promising therapeutic advantages for further development.

Keto-enol tautomerism of β-diketo molecules in the presence of graphitic materials through π-π stacking

The pseudo aromatic structures of the enol forms of β-diketo molecules are stabilized on the surface of graphitic materials through π-π interaction. This phenomenon has been studied through a relative binding energy calculation using density functional theory. The intermolecular interaction as well as the relative stability of the keto or enol tautomer is also influenced by the functional groups attached to the graphitic materials. The theoretical results are supported by spectroscopic evidence. Our study with three different graphitic materials, with a comparable extent of π-electrons and acid functionalities, reveals that π-π interaction is the main governing factor for the stability of the enol forms. Then comes the role of intermolecular H-bonding between the adsorbate and adsorbent. This can stabilize both the keto and enol tautomers, according to the arrangements of the functional groups and the geometry of the β-diketo molecules. Acid groups on the adsorbent can enhance enolization through H-bonding, but an excess of functional groups may decrease the possibility of π-π interaction by disrupting the π-clouds of the graphitic surface and pushing the adsorbate and adsorbent away from each other beyond a π-π stacking distance. In that situation, H-bonding becomes crucial for determining the relative stability. Our results indicate that graphitic materials with acid functionalities across their edges, and ample π-cloud, are the most suitable catalysts for enolization.

Assessment of antidiabetic activity of three Phenylspirodrimanes from fungus Stachybotrys chartarum MUT 3308 by ADME, QSAR, molecular docking and molecular dynamics simulation studies against protein tyrosine phosphatase 1B (PTP1B)

Phenylspirodrimanes (PSD) are the sesquiterpene quinone type meroterpenoids found in nature. PSDs are found to exhibit inhibitory activity against immunocomplex diseases, and tyrosine kinase receptors. Three of the different PSDs C1, C2, and C3 that have been reported to be isolated from the sponge-associated fungus Stachybotrys chartarum MUT 3308 are selected for studying their possible inhibitory effect against type 2 diabetes mellitus. Mechanistically, blocking protein tyrosine phosphatase 1B (PTP1B) helps to reduce the insulin resistance induction caused by the high expression of PTP1B. The QSAR, ADME, toxicity (T) study was carried out to predict the pharmacokinetic properties and the biological activities of the PSDs. PASS prediction web tool was used to find and select the target proteins 1NNY, and 2HNP. According to the molecular docking simulations, C1 and C2 showed better binding affinity of -8.5 kcal/mol, and -8.1 kcal/mol respectively against 1NNY compared to the control ligand. RMSD, RMSF, Rg, and SASA analysis revealed that both C1, and C2 showed better stability, minor conformational changes, and minor fluctuation upon binding to PTP1B. Protein contact analysis was carried out to validate the residues that are in contact with the ligands according to molecular docking studies. Overall, C1, and C2 could be proposed as novel natural hits to be developed and small modifications of these PSDs could result in inducing the binding affinity significantly, although experimental validation is required for further evaluation of the work.Communicated by Ramaswamy H. Sarma.

Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules

The electronic properties of DNA molecules, defined by the sequence-dependent ionization potentials of nucleobases, enable long-range charge transport along the DNA stacks. This has been linked to a range of key physiological processes in the cells and to the triggering of nucleobase substitutions, some of which may cause diseases. To gain molecular-level understanding of the sequence dependence of these phenomena, we estimated the vertical ionization potential (vIP) of all possible nucleobase stacks in B-conformation, containing one to four Gua, Ade, Thy, Cyt, or methylated Cyt. To do this, we used quantum chemistry calculations and more precisely the second-order Møller-Plesset perturbation theory (MP2) and three double-hybrid density functional theory methods, combined with several basis sets for describing atomic orbitals. The calculated vIP of single nucleobases were compared to experimental data and those of nucleobase pairs, triplets, and quadruplets, to observed mutability frequencies in the human genome, reported to be correlated with vIP values. This comparison selected MP2 with the 6-31G* basis set as the best of the tested calculation levels. These results were exploited to set up a recursive model, called vIPer, which estimates the vIP of all possible single-stranded DNA sequences of any length based on the calculated vIPs of overlapping quadruplets. vIPer's vIP values correlate well with oxidation potentials measured by cyclic voltammetry and activities obtained through photoinduced DNA cleavage experiments, further validating our approach. vIPer is freely available on the github.com/3BioCompBio/vIPer repository.

Towards control of excitonic coupling in DNA-templated Cy5 aggregates: the principal role of chemical substituent hydrophobicity and steric interactions

Understanding and controlling exciton coupling in dye aggregates has become a greater focus as potential applications such as coherent exciton devices, nanophotonics, and biosensing have been proposed. DNA nanostructure templates allow for a powerful modular approach. Using DNA Holliday junction (HJ) templates variations of dye combinations and precision dye positions can be rapidly assayed, as well as creating aggregates of dyes that could not be prepared (either due to excess or lack of solubility) through alternative means. Indodicarbocyanines (Cy5) have been studied in coupled systems due to their large transition dipole moment, which contributes to strong coupling. Cy5-R dyes were recently prepared by chemically modifying the 5,5'-substituents of indole rings, resulting in varying dye hydrophobicity/hydrophilicity, steric considerations, and electron-donating/withdrawing character. We utilized Cy5-R dyes to examine the formation and properties of 30 unique DNA templated homodimers. We find that in our system the sterics of Cy5-R dyes play the determining factor in orientation and coupling strength of dimers, with coupling strengths ranging from 50-138 meV. The hydrophobic properties of the Cy5-R modify the percentage of dimers formed, and have a secondary role in determining the packing characteristics of the dimers when sterics are equivalent. Similar to other reports, we find that positioning of the Cy5-R within the HJ template can favor particular dimer interactions, specifically oblique or H-type dimers.

Synthesis and Optical Properties of a Series of Push-Pull Dyes Based on Pyrene as the Electron Donor

Fifteen push-pull dyes comprising the tetracyclic polyaromatic pyrene have been designed and synthesized. The optical properties of the fifteen dyes have been examined in twenty-two solvents of different polarities. Surprisingly, contrarily to what is classically observed for push-pull dyes of D-π-A structures, a negative solvatochromism could be found for numerous dyes. The photoluminescence and thermal properties of the dyes were also examined. Theoretical calculations were carried out to support the experimental results.

Human health risk assessment of cinnamate UV absorbers: In vitro and in silico investigations

Organic UV absorbers (UVAs) are contaminants of emerging concern. Environmental persistence and potential toxicological enrichment studies of UVAs have attracted international concern. It is important to study the toxicity mechanism of UVAs. This study is the first to report the toxicological mechanism of two cinnamate UV absorbers (CUVAs), 2-ethyl 4-methoxycinnamate (OMC) and isoamyl 4-methoxycinnamate (IMC) based on cellular models and molecular models. Cellular models demonstrated that the CUVAs-induced apoptosis might be associated with cellular mitochondrial damage pathways. The results of molecular models showed that OMC and IMC could affect the binding between major proteins and enzymes in the mitochondrial damage pathway and contaminants, ultimately leading to apoptosis. The cellular-molecular models showed that IMC and OMC have dose-effect relationships on cytotoxicity. The composite model is more informative than a single model. This study further indicate that UVAs causes toxicology effects that have implications for the environment and human health.

Detection and binding interactions of pharmaceutical contaminants using quartz crystal microbalance - Role of adsorbate structure and surface functional group on adsorption

HYPOTHESIS

Emerging contaminants (ECs) can interact with soft solid/aqueous interfaces of particulate organic matter and microplastics in the aquatic environment but to what extent? It is hypothesized that EC adsorption can be detected using quartz crystal microbalance (QCM), a sensitive gravimetric tool, and their adsorption energetics and uptake capacity can be measured for various substrates of distinct functional group. This in turn reveals the specific vs. nonspecific interactions.

EXPERIMENTS

QCM has been used to detect and measure the adsorption of selected pharmaceuticals, amlodipine (AMP) and carbamazepine (CBZ), onto butyl, carboxyl, amine, and phenyl functionalized self-assembled monolayers (SAMs), mapping out the hydrophobic effect, H-bonding capability, and π- interactions. Adsorption free energy (ΔGads) and maximum interfacial concentration (cmax) for these surfaces are compared. Solvatochromic studies to elucidate the likelihood of H-bonding interactions for CBZ and AMP have been conducted using UV-Vis absorption spectroscopy.

FINDINGS

Amlodipine and carbamazepine adsorb onto butyl/aqueous interface with respective ΔGads values of -35.8 ± 1.1 and -37.7 ± 0.1 kJ/mol. Nonspecific interaction allows a greater extent of cmax on the hydrophobic/aqueous interface. CBZ does not bind to the phenyl surface. AMP and CBZ exhibit H-bonding and show proclivity for the amine and carboxyl SAMs. Interfacial chemical environment and adsorbate structural properties play a significant role on EC adsorption.

Droplet-based microfluidic synthesis of nanogels for controlled drug delivery: tailoring nanomaterial properties via pneumatically actuated flow-focusing junction

Conventional batch syntheses of polymer-based nanoparticles show considerable shortcomings in terms of scarce control over nanomaterials morphology and limited lot-to-lot reproducibility. Droplet-based microfluidics represents a valuable strategy to overcome these constraints, exploiting the formation of nanoparticles within discrete microdroplets. In this work, we synthesized nanogels (NGs) composed of hyaluronic acid and polyethyleneimine using a microfluidic flow-focusing device endowed with a pressure-driven micro-actuator. The actuator achieves real-time modulation of the junction orifice width, thereby regulating the microdroplet diameter and, as a result, the NG size. Acting on process parameters, NG hydrodynamic diameter could be tuned in the range 92-190 nm while preserving an extremely low polydispersity (0.015); those values are hardly achievable in batch syntheses and underline the strength of our toolbox for the continuous in-flow synthesis of nanocarriers. Furthermore, NGs were validated in vitro as a drug delivery system in a representative case study still lacking an effective therapeutic treatment: ovarian cancer. Using doxorubicin as a chemotherapeutic agent, we show that NG-mediated release of the drug results in an enhanced antiblastic effect vs. the non-encapsulated administration route even at sublethal dosages, highlighting the wide applicability of our microfluidics-enabled nanomaterials in healthcare scenarios.

Intermolecular Interactions of Pyrene and Its Oxides in Toluene Solution

In this work, the conformer-rotamer ensemble sampling tool (CREST), with the underlying semiempirical GFN2-xtb method, was used for automated geometry exploration of the homodimers of pyrene, pyrene-4,5-dione, and pyrene-4,5,9,10-tetraone, along with the heterodimer of pyrene and pyrene-4,5,9,10-tetraone. Geometries and energies of the dimers were further refined at the ωB97X-D4/def2-TZVP level of theory, both in the gas phase and in toluene solution. Computations in solution were handled using the CPCM (conductor-like polarizible continuum model) and SMD (solvation model based on density) models. Two previously unidentified pyrene-homodimer conformations were identified, and the effects of oxidation on the geometries and energies of dimerization were explored; in general, oxidation leads to stronger intermolecular interactions and decreased solubility in toluene. For selected dimers, DLPNO-CCSD(T)/cc-pVTZ/SMD(Toluene) energies were determined at the DFT geometries and illustrated the accuracy of the ωB97X-D4 approach, with an MAD of 1.47 kJ/mol.

Electrostatic penetration effects stand at the heart of aromatic π interactions

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

Pyridine interaction with γ-CuI: synergy between molecular dynamics and molecular orbital approaches to molecule/surface interactions

We have used a synergistic computational approach merging Molecular Dynamics (MD) simulations with density functional theory (DFT) to investigate the mechanistic aspects of chemisorption of pyridine (Py) molecules on copper iodide. The presence of both positive and negative ions at the metal halide surface presents a chemical environment in which pyridine molecules may act as charge donors and/or acceptors. Computational results reveal that Py molecules interact with the γ-CuI(111) surface owing to a combination of noncovalent Cu⋯N, Cu/I⋯π/π*, and hydrogen bonding interactions as determined via Natural Bonding Orbitals (NBO). Introduction of surface defect sites alters the interaction dynamics, resulting in a "localizing effect" in which the Py molecules clump together within the defect site. Significant enhancement of hydrogen bonding between C-H σ* and I 6p orbitals results in more tightly surface-bound Py molecules. Our findings provide a platform for understanding the interaction between Py and Py-derivative vapors and metal-based surfaces that contain both electron acceptor and donor atoms.

AromTool: predicting aromatic stacking energy using an atomic neural network model

Aromatic stacking exists widely and plays important roles in protein-ligand interactions. Computational tools to automatically analyze the geometry and accurately calculate the energy of stacking interactions are desired for structure-based drug design. Herein, we employed a Behler-Parrinello neural network (BPNN) to build predictive models for aromatic stacking interactions and further integrated it into an open-source Python package named AromTool for benzene-containing aromatic stacking analysis. Based on extensive testing, AromTool presents desirable precision in comparison to DFT calculations and excellent efficiency for high-throughput aromatic stacking analysis of protein-ligand complexes.

The σ-hole⋯σ-hole stacking interaction: An unrecognized type of noncovalent interaction

The σ-hole⋯σ-hole stacking interaction, an unrecognized type of noncovalent interaction, has been found to be present in large quantities in the Cambridge Structural Database. In the σ-hole⋯σ-hole stacking interaction, each of the two interacting σ-holes has the dual electron donor/electron acceptor character; when one σ-hole acts as an electron donor, the other σ-hole acts as an electron acceptor, and vice versa. The σ-hole⋯σ-hole stacking interaction is clearly different from the σ-hole bond in which the charge transfer occurs mainly from the electron donor to the σ-hole. Energy component analysis shows that the σ-hole⋯σ-hole stacking interaction is dominated by the dispersion energy, which is similar to the nature of the aromatic stacking interaction between unsaturated molecules or the σ⋯σ stacking interaction between saturated molecules.

Reinterpreting π-stacking

The nature of π-π interactions has long been debated. The term "π-stacking" is considered by some to be a misnomer, in part because overlapping π-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered "slip-stacked" motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate π-π interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic saturated hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic π-π interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked π-π architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize π-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp² carbon networks lead to attractive interactions that are "served up on a molecular pizza peel", and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformational landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for π-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked π-π motif in protein crystal structures.

Catalysis on Pristine 2D Materials via Dispersion and Electrostatic Interactions

Shape complementarity between catalyst and transition state structure is one of the cornerstones of chemical catalysis. Likewise, noncovalent interactions play a major role in catalysis. It has been predicted computationally and recently confirmed experimentally [Kroeger, A. A.; Hooper, J. F.; Karton, A. ChemPhysChem, 2020, 21, 1675-1681] that pristine graphene can efficiently catalyze chemical processes via π-interactions and shape complementarity. Here we show that other two-dimensional materials with different electronic structures and chemical compositions (h-BN and graphane) can also catalyze chemical processes that proceed via planar transition state structures. These include the bowl-to-bowl inversions in corannulene and sumanene and the rotation about the C-C bond in substituted biphenyls. This catalytic activity is achieved through shape complementarity between planar nanomaterial and planar transition state structure, enabling disproportionate stabilization of the transition state structures over the nonplanar reactants and products. A DFT-based energy decomposition analysis shows that this catalytic activity is mainly driven by dispersion and electrostatic forces, which together outweigh the Pauli repulsion term. These findings enrich and expand the concept of catalysis by pristine 2D materials.

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.

What Is Special about Aromatic-Aromatic Interactions? Significant Attraction at Large Horizontal Displacement

High-level ab initio calculations show that the most stable stacking for benzene-cyclohexane is 17% stronger than that for benzene-benzene. However, as these systems are displaced horizontally the benzene-benzene attraction retains its strength. At a displacement of 5.0 Å, the benzene-benzene attraction is still ∼70% of its maximum strength, while benzene-cyclohexane attraction has fallen to ∼40% of its maximum strength. Alternatively, the radius of attraction (>2.0 kcal/mol) for benzene-benzene is 250% larger than that for benzene-cyclohexane. Thus, at relatively large distances aromatic rings can recognize each other, a phenomenon that helps explain their importance in protein folding and supramolecular structures.

Curvature and size effects hinder halogen bonds with extended π systems

The curvature of aromatic systems strengthens the interaction by the concave face while it weakens by the convex one. Parallel structures are favoured over halogen bonded ones.

Distinct Crystalline Aromatic Structural Motifs: Identification, Classification, and Implications

Spatial noncovalent helical organization of nucleobases in DNA and radial organization of chromophores in natural light-harvesting systems are fascinating yet enigmatic. Understanding the numerous weak interactions that drive the formation of elegant supramolecular architectures in native natural systems and developing bioinspired design strategies have seen a surge of interest in recent decades. Self-assembly of functional chromophores in the crystalline phase is a definitive strategy to identify novel molecule-molecule interactions, in particular, atom-atom interactions, and to understand the synergistic nature of noncovalent interactions that stabilizes the supramolecular organization. This Account narrates our recent efforts in developing desirable supramolecular motifs employing weak interaction-based strategies and our observation of deviations from the common motifs chartered in aromatic systems. Modulation of long-range aromatic interactions through chemical modifications (acylation, benzoylation, haloacylation, and alkylation of chromophores) to attain a preferred stacking (herringbone, lamellar, or columnar) is presented. Particular attention has been given to attaining lamellar or columnar packing possessing potential interchromophoric electronic coupling mediated high charge mobility. Supramolecular arrangements of noncovalently or covalently associated donor-acceptor systems that open up additional possibilities of packing modes (segregated, mixed etc.) are explored. Our persistent efforts yielded distinct twisted-segregated and alternate distichous stacks for the nonparallel covalently linked donor-acceptor systems that favor a long-lived photoinduced charge-separated state. We further move on to discuss the unconventional packing motifs that were identified recently. The highly sought-after Greek cross (+) stacking of chromophores in crystalline phase and an elegant crystalline radial arrangement of chromophores are examined. The Greek cross (+) stacked architecture exhibits monomer-like emission characteristics owing to the absence of exciton coupling across the orthogonally stacked chromophores. Crystalline helical chromophore assembly is yet another emerging motif with far-reaching applications in domains ranging from asymmetric catalysis to chiral smart materials and has been accounted here by citing certain phenomenal examples from literature. Thus, this Account demonstrates that identifying and classifying new structural motifs based on topological aspects, such as interchromophoric orientation (cross) and extended chromophore arrangement in the crystal lattice (radial, helical, etc.), are crucial since such fundamental characteristics dictate the properties emerging out of the corresponding motifs. Encouraged from ours and others' works, we propose the addition of new aromatic supramolecular structural motifs, namely, cross-stacked, helical, and radial arrangements, in order to expand the classification. We believe that identifying new emergent property-based supramolecular motifs and investigating the methods to achieve the desired motif will eventually have implications in fundamental crystal engineering, supramolecular chemistry, and biomimetic design of functional materials.

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.

Null Exciton Splitting in Chromophoric Greek Cross (+) Aggregate

Exciton interactions in molecular aggregates play a crucial role in tailoring the optical behaviour of π-conjugated materials. Though vital for optoelectronic applications, ideal Greek cross-dipole (α=90°) stacking of chromophores remains elusive. We report a novel Greek cross (+) assembly of 1,7-dibromoperylene-3,4,9,10-tetracarboxylic tetrabutylester (PTE-Br₂ ) which exhibits null exciton coupling mediated monomer-like optical characteristics in the crystalline state. In contrast, nonzero exciton coupling in X-type (α=70.2°, PTE-Br₀ ) and J-type (α=0°, θ=48.4°, PTE-Br₄ ) assemblies have perturbed optical properties. Additionally, the semi-classical Marcus theory of charge-transfer rates predicts a selective hole transport phenomenon in the orthogonally stacked PTE-Br₂ . Precise rotation angle dependent optoelectronic properties in crystalline PTE-Br₂ can have consequences in the rational design of novel π-conjugated materials for photonic and molecular electronic applications.