Aromatic Stacking Interactions Research Articles

Hyper-crosslinked polymers with controlled multiscale porosity for effective removal of benzene from cigarette smoke

Abstract A series of hyper-crosslinked polymers (HCPs) with connected hierarchical porous structures were synthesized from phenyl-based precursors of benzene (BEN), benzyl alcohol, aniline, biphenyl, and 1,3,5-triphenylbenzene (TPB) via the knitting method. The porous structures of the HCPs were greatly influenced by substituent groups and BEN ring number in the precursors. HCPs prepared from TPB had the largest surface area and pore volume with multiscale porosity. The porous structure of the HCPs could also be adjusted by the crosslinker amount. Insufficient crosslinking led to incomplete pore architecture, while excessive crosslinking resulted in a considerable decrease in the pore volume. With these HCPs as adsorbents, the BEN yield in the cigarette smoke could be largely reduced due to the connected multiscale porosity and π–π aromatic stacking interaction that facilitated the smoke aerosol passing and the small aromatic molecules absorbing, showing great potential of these HCPs as adsorbents for effective removal of BEN from cigarette smoke.

Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases.

Methylation and demethylation of DNA, RNA and proteins constitutes a major regulatory mechanism in epigenetic processes. Investigations would benefit from the ability to install photo‐cleavable groups at methyltransferase target sites that block interactions with reader proteins until removed by non‐damaging light in the visible spectrum. Engineered methionine adenosyltransferases (MATs) have been exploited in cascade reactions with methyltransferases (MTases) to modify biomolecules with non‐natural groups, including first evidence for accepting photo‐cleavable groups. We show that an engineered MAT from Methanocaldococcus jannaschii (PC‐MjMAT) is 308‐fold more efficient at converting ortho‐nitrobenzyl‐(ONB)‐homocysteine than the wildtype enzyme. PC‐MjMAT is active over a broad range of temperatures and compatible with MTases from mesophilic organisms. We solved the crystal structures of wildtype and PC‐MjMAT in complex with AdoONB and a red‐shifted derivative thereof. These structures reveal that aromatic stacking interactions within the ligands are key to accommodating the photocaging groups in PC‐MjMAT. The enlargement of the binding pocket eliminates steric clashes to enable AdoMet analogue binding. Importantly, PC‐MjMAT exhibits remarkable activity on methionine analogues with red‐shifted ONB‐derivatives enabling photo‐deprotection of modified DNA by visible light.

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

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

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

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

Self-Assembly of Peptide Hierarchical Helical Arrays with Sequence-Encoded Circularly Polarized Luminescence.

Self-assembled peptide materials with sequence-encoded properties have attracted great interest. Despite their intrinsic chirality, the generation of circularly polarized luminescence (CPL) based on the self-assembly of simple peptides has been rarely reported. Here, we report the self-assembly of peptides into hierarchical helical arrays (HHAs) with controlled supramolecular handedness. The HHAs can emit full-color CPL signals after the incorporation of various achiral fluorescent molecules, and the glum value is 40 times higher than that of the CPL signal from the solutions. By simply changing the amino acid sequence of the peptides, CPL signals with opposite handedness can be generated within the HHAs. The peptide HHAs can provide hydrophobic pockets to accommodate the fluorescent molecules with helical arrangement through strong aromatic stacking interactions, which are responsible for the CPL signals. This work provides a pathway to construct highly ordered chiral materials, which have broad applications in the chiroptical field.

Bis-Pyrene Photo-Switch Open- and Closed-Form Differently Bind to ds-DNA, ds-RNA and Serum Albumin and Reveal Light-Induced Bioactivity.

Newly designed and synthesized diarylethene (DAE) derivatives with aliphatic amine sidearms and one with two pyrenes, revealed excellent photo-switching property of central DAE core in MeOH and water. The only exception was bis-pyrene analogue, its DAE core very readily photochemically closed, but reversible opening completely hampered by aromatic stacking interaction of pyrene(s) with cyclic DAE. In this process, pyrene fluorescence showed to be a reliable monitoring method, an open form characterized by strong emission at 480 nm (typical for pyrene-aggregate), while closed form emitted weakly at 400 nm (typical for pyrene-DAE quenching). Only open DAE-bis-pyrene form interacted measurably with ds-DNA/RNA by flexible insertion in polynucleotide grooves, while self-stacked closed form did not bind to DNA/RNA. For the same steric reasons, flexible open DAE-bis-pyrene form was bound to at least three different binding sites at bovine serum albumin (BSA), while rigid, self-stacked closed form interacted dominantly with only one BSA site. Preliminary screening of antiproliferative activity against human lung carcinoma cell line A549 revealed that all DAE-derivatives are non-toxic. However, bis-pyrene analogue efficiently entered cells and located in the cytoplasm, whereby irradiation by light (315–400 nm) resulted in a strong, photo-induced cytotoxic effect, typical for pyrene-related singlet oxygen species production.

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T-A and U-A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

Crystal Structures of a Melibiose Symporter MelB with Bound Sugar Substrate

MelB is a well-studied symporter from the major facilitator superfamily of transporters, and its mammalian homologues play important roles in the delivery of essential omega-3 fatty acids into brain and eyes. The bacterial MelB is selective for galactose or galactosides, and catalyzes the obligatory cotransport of the sugar with Na+, Li+, or H+. Previous 3-D crystal structure of the MelBSt of Salmonella thyphimurium shows that MelB adopts a typical MFS-fold, and the thermodynamic ligand binding studies reveal that cooperative binding of Na+ and melibiose is the core mechanism for the obligatory symport. To gain insights into the substrate binding, we solved three sugar-bound crystal structures from two MelBSt mutants that are compromised on Na+ binding. The structures with bound nitrophenyl-α-D-galactoside or melibiose-based detergent dodecyl-β-d-melibioside (DDMB) were refined to a resolution between 3.05 - 3.25 Å. All three structures are nearly identical at an outward-facing conformation; each one contains a á-galactoside molecule in the middle of protein. The binding interactions of galactosyl moiety from each ligand are indistinguishable, revealing a selection pocket, and the non-galactosyl moieties occupy differently. The active site displays a strong salt-bridge/hydrogen-bonding network that provides multiple polar interactions to each of four OH groups on the galactosyl moiety, and the galactosyl ring is sandwiched by two aromatic sidechains via aromatic stacking interactions. There is little or no interaction toward the non-galactosyl moieties, and the entire 12-carbon tail of DDMB lies within the internal cavity. The localized interactions towards the specific galactosyl moiety and the large internal cavity allow MelB to accommodate a variety of galactosides with different structures. The proposed Na+-binding pocket with no bound Na+ seems to lie in a close proximity to the bound sugar. These structures represent a Na+-free, galactoside-bound binary complex of MelB.

Gas-Induced Phase Transition of Dipeptide Supramolecular Assembly

Gas-Induced Phase Transition of Dipeptide Supramolecular Assembly

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.

Theoretical Investigation of the Inhibitory Mechanism of Norepinephrine on hIAPP Amyloid Aggregation and the Destabilization of Protofibrils.

The search for an appropriate drug to completely eradicate type II diabetes (T2D), a metabolic disorder from which over 40 million people suffer worldwide, has not yet led to any satisfactory result. The misfolding of human islet amyloid polypeptide (hIAPP) into toxic oligomers is a pathogenic feature of this disease, due to which the prevention of hIAPP aggregation is considered the rational approach to combat T2D. Hence, we study the role of a catecholamine, norepinephrine, on the amyloid aggregation of hIAPP, which has previously displayed inhibitory effect on amyloid-β aggregation. Via all-atom molecular dynamics simulations, we observe that norepinephrine can not only inhibit the aggregation of hIAPP but also partially disassemble the preformed fibrils. For comparison, the influence of two other molecules (aspirin and benzimidazole, both of which have previously reported to have no inhibitory impact on hIAPP aggregation) is also analyzed. We observe that the conformational preference of hIAPP changes from a β-sheet conformation to a disordered state when norepinephrine is added to the peptides. However, no such effect is observed in the presence of aspirin or benzimidazole. In-depth investigation reveals that the β-sheets formed between Leu12-His18 and Leu27-Gly33 enhance the peptide-peptide interactions that are broken by norepinephrine, which itself interacts with the peptides via hydrogen bonding, hydrophobic, and aromatic stacking interactions, preferentially with the C-terminal residues of hIAPP. The molecular mechanism action of norepinephrine on hIAPP aggregation can provide useful insight for the drug design against T2D.

Relative Contributions of Base Stacking and Electrostatic Repulsion on DNA Nicks and Gaps.

In duplex DNA, the continuous sugar phosphate backbones prevent the double helix from significant bending, but breaks in the duplex such as nicks, gaps, and flaps present points at which significant bending is possible. The conformational dynamics of these aberrant structures remains poorly understood. Two factors can maintain the duplexlike conformation of these aberrant structures, these being the hydrophobic and aromatic stacking interactions of the nucleobases, and the electrostatic repulsion of the negatively charged backbones. Using confocal single-molecule Förster resonance energy transfer on nicked and gapped DNA structures, we compare the relative contributions of these two factors by modulating the electrostatic repulsion through mono- and divalent cation concentrations. Base stacking interactions dominate the dynamics of nicked DNA, making it behave essentially like duplex DNA. Gapped structures have weaker base stacking and thus backbone electrostatic repulsion becomes important, and shielding from cations results in an average increase in bending around the gap. This bending of gapped structures could be interpreted by increased flexibility of unstacked structures, transient unstacking events, or a combination of the two. Burst variance analysis (BVA) and analysis by photon-by-photon hidden Markov modeling (H2MM), methods capable of detecting submillisecond dynamics of single molecules in solution, only revealed a single state, indicating that dynamics are occurring at time scales shorter than microseconds.

Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor.

Human interleukin-6 (hIL-6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL-6 binding to the IL-6 receptor (IL-6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti-IL-6 and IL-6R antibodies are clinically approved inhibitors of IL-6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL-6 antagonists derived from understanding the structural basis for IL-6/IL-6Rα interactions. Here, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL-6 with IL-6Rα. A comparison with MD of apo hIL-6 reveals that the binding of hIL-6 to IL-6Rα induces structural and dynamic rearrangements in the AB loop region of hIL-6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL-6)- Glu182 (IL-6Rα) and Arg184 (hIL-6)- Glu183 (IL-6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL-6/IL-6Rα complex.

Evaluation of Amaryllidaceae alkaloids as inhibitors of human acetylcholinesterase by QSAR analysis and molecular docking

There currently are a large number of natural products of plant origin that have potential use in the treatment of Alzheimer's disease. One of the most commonly used drugs for the treatment of this disease contains the galantamine alkaloid isolated from amaryllidine plants as an active ingredient, whose action lies in the inhibition of acetylcholinesterase (AChE). For this reason, it is promising to evaluate other alkaloids from this family of plants. In the present investigation, the inhibitory activity of human AChE by alkaloids of amaryllidic species registered in the PubChem and Reaxys chemical databases was evaluated through the development of 4 qualitative QSAR models. The models were based on the random forest algorithm using the calculated descriptors in Volsurf + and DRAGON of compounds that had reported AChE inhibitory activity in the ChEMBL and NPASS databases. From the QSAR models, 11 alkaloids with the highest inhibitory potential were obtained. Molecular docking analysis was used to examine the interactions of these 11 alkaloids with various residues of the protein active site. Overall, 23 representative descriptors were reported whose interpretation allowed to identify several properties that confer inhibitory potential against human AChE, in fact, the presence of amine groups, hydroxyl groups and aromatic rings in fused cycles are able to shape prolated and planar geometries are significant for hydrogen bond and aromatic stacking interactions in the active site of human AChE. Among the 11 alkaloids founded, lycoramine showed the highest inhibitory potential, and masonine presented interactions in the CAS (Catalytic Anionic Site) and PAS (Peripheral Anionic Site). Therefore, these compounds could be potential unconventional inhibitors of AChE.

Construction of three-dimensional interleaved protein hetero-superlattices in solution by cooperative electrostatic and aromatic stacking interactions

HypothesisHierarchical assembly of naturally occurring assemblies is accurate and responsible for performing various cellular functions. However, Nature’s wisdom in navigating the assembly process to desired protein assemblies by the cooperation of multiple noncovalent interactions has been underexploited for protein superstructures constructions. Owing to the chemical diversity of noncovalent interactions, it should be possible to fabricate protein assemblies with novel properties in high efficiency through the cooperation of different noncovalent interaction. ExperimentsBoth charged residues and aromatic residues are introduced on the exterior surface of ferritin centered at their symmetry axes, mixing of complementary variants forms ordered assemblies through the cooperation of two kinds of chemical-diverse noncovalent interactions. The assemblies were further characterized in terms of their assembly behavior, structure, size, assembly kinetics, properties and stabilities. FindingsWe utilized both electrostatic and π-π stacking interactions between complementary nanocages to cooperatively trigger the self-assembly into predesigned interleaved hetero-superlattices which exhibit high electrolyte stability and thermal stability. The size of the hetero-superlattices can be well controlled with ranges from nanometers to micrometers in solution in response to external stimuli such as pH and salt concentration. The hetero-superlattice may have the potential applications in hybrid bio-templating, light-harvesting and compartmentalized encapsulation.

Role of Thermolysin in Catalytic-Controlled Self-Assembly of Fmoc-Dipeptides

In recent years, short peptide self-assembled materials, prepared under the control of the thermolysin catalyst, have been investigated extensively and shown to acquire various morphologies and fun...

Study on the self-assembly behaviors based on aromatic carboxylic acids and dibenzo-diaza-crown ether salts

Pyromellitic acid (pmaH4) with N,N′-dibutyl-diaza-18-crown-6 (3), N,N′-di(2-ethoxyethyl)-diaza- 18-crown-6 (4), N,N′-di(2-butoxyethyl)-diaza-18-crown-6 (5), N,N′-di(2-(2-butoxyethoxy)ethyl)-diaza-18- crown-6 (6) and picric acid (paH) with N,N′-di(2-(2-butoxyethoxy)ethyl)-diaza-18-crown-6 (6) have been obtained as single crystals in crystallization solvent acetone-water. Single crystal X-ray diffraction studies show that organic acid-aza crown ether co-crystals are proton-transfer organic salts. In every pyromellitic acid with aza-crown ether organic salts, acid and base are present in a 1:1 ratio, and the charge-assisted ((N+) N–H⋯O (COO−)) hydrogen bonds and aromatic stacking interactions (π···π stacking) provides the main forces to direct the packing modes of molecules together. Acid and base are present in a 2:1 ratio in the picric acid with compound 6 organic salts, and aromatic stacking interactions provide direct binding of pa anions with aza-crown ether cations. The supramolecular structures of organic salts are also supported by other non-covalent interactions, such as O···π stacking, C–H···π interaction and C–H⋯O interactions. Small molecules (water or acetone) wrapped in the crystals can effectively help to build the supramolecular structures of these organic salts.

A co-crystal strategy for the solidification of liquid pyrazine derivatives: X-ray structures and Hirshfeld surface analyses

Here we described a co-crystal strategy for the solidification of liquid 2,3-dimethylpyrazine (2,3-DMP), 2,5-dimethylpyrazine (2,5-DMP), 2,6-dimethylpyrazine (2,6-DMP) with the poly-substituted salicylic acids [3,5,6-trichlorosalicylic acid (TCSA) and 3,5-dinitrosalicylic acid (DNSA)] under identical conditions. Those newly grown co-crystals (2,3-DMP:TCSA = 1:1 for 1; 2,5-DMP:TCSA = 1:2 for 2; 2,6-DMP:DNSA = 1:1 for 3) were characterized by single-crystal X-ray diffraction. The structure determination shows that strong O-H⋯N hydrogen bonds play an important role in connection of pyrazine derivatives and poly-substituted salicylic acids. Moreover, aromatic cycle stacking interactions play a crucial role in the 3D supramolecular network. Hirshfeld surfaces and fingerprint plots of the reported co-crystals were analyzed, which showed that O-H⋯N, C-H⋯O, H⋯H, H⋯Cl and aromatic cycle stacking intermolecular interactions are the main stabilizing factors of the co-crystal structures. The melting points studies showed that the co-crystal strategy is effective for solidification of liquid pyrazine derivatives.

Insights from electron density analysis into the charge transfer mechanism in a photoluminescent cocrystal of phenanthrene and tetrafluoro-1,4-benzoquinone

Theoretical charge density studies are performed on the photoluminescent co-crystal of phenanthrene (PHNT) and tetrafluoro-1,4-benzoquinone (TFBQ) using the multipole modelling of theoretical structure factors. The topological analysis of the electron density is performed for all intramolecular covalent bonds and various important intermolecular interactions in the solid state. In addition to the presence of C–H⋯F interactions, the presence of aromatic stacking interactions has been confirmed via bond paths, topological properties and electrostatic potential isosurfaces of the electron density. The stacking interactions between the electron deficient and electron rich aromatic rings are demonstrated using the net atomic charges and electrostatic potential isosurfaces, which is responsible for the observed photoluminescent properties of the co-crystal. The molecular orbitals involved in the electronic transitions during UV–vis spectroscopic measurements have been identified and the electron density difference maps (EDDMs) arising from these transitions to different excited states have been plotted on isosurfaces which is in agreement with the Charge-Transfer (CT) nature of this co-crystal.

Antimicrobial screening and pharmacokinetic profiling of novel phenyl-[1,2,4]triazolo[4,3-a]quinoxaline analogues targeting DHFR and E. coli DNA gyrase B

A novel series of [1,2,4]triazolo[4,3-a]quinoxaline derivatives of different heteroaromatization members were synthesized. The newly synthesized molecules were explored for their potential antimicrobial activities against a panel of pathogenic organisms. Among these derivatives, the chalcone compound 6e with a methoxy substituent exhibited broad potent antimicrobial activity against most of the bacterial and fungal strains. Furthermore, the analysis of the SAR disclosed that the linker and terminal aromatic fragments perform critical roles in exerting antibacterial activity. The molecular docking calculations were executed on two of the most bacterial targets, ATP-binding sites of DNA gyrase B, and the folate-binding site of DHFR enzymes. The results presented good binding data to the pockets of both enzymes showing different linkers contributions through the hydrogen-bonding and aromatic stacking interactions that stabilize the compounds in their pockets taking 6e compound as representative of most active analogs. In addition, good pharmacokinetic profiling data for the 6e compound was obtained and compared to reference drugs. Accordingly, our findings suggest that [1,2,4]triazolo[4,3-a]quinoxaline scaffold is an interesting precursor for the design of potent antimicrobial agents with multitarget inhibition.