π-Stacked Dimers of Fluorophenylacetylenes: Role of Dipole Moment

Correlating π-π Stacking of Aromatic Diammoniums with Stability and Dimensional Reduction of Dion-Jacobson 2D Perovskites

Dion-Jacobson (DJ) phase 2D perovskites with various aromatic diammonium cations, potentially possessing high stability, have been developed for optoelectronics. However, their stability does not meet initial expectations, and some of them even easily degrade into lower-dimensional structures. Underlying the stability mechanism and dimensional reduction of these DJ 2D perovskites remains elusive. Herein, we report that π-π stacking intensity between aromatic cations determines structural stability and dimensional variation of DJ 2D perovskites by investigating nine benzene diammoniums (BDAs)-derived low-dimensional perovskites. The BDAs without intermolecular π-π stacking form stable DJ 2D perovskites, while those showing strong π-π stacking tend to generate 1D and 0D architectures. Furthermore, the π-π stacking intensity highly relies on molecular symmetry and electrostatic potential of BDAs; namely, asymmetry and small dipole moment facilitate alleviating the π-π stacking, leading to the formation of DJ 2D perovskites and vice versa. Our findings establish the relationship of aromatic diammonium structure-π-π stacking interaction-perovskite dimensionality, which can guide the design of stable DJ 2D perovskites and the manipulation of perovskite dimensionality for various optoelectronic applications.

Tuning Electrostatic and Hydrophobic Surfaces of Aromatic Rings to Enhance Membrane Association and Cell Uptake of Peptides

Aromatic groups are key mediators of protein–membrane association at cell surfaces, contributing to hydrophobic effects and π‐membrane interactions. Here we show electrostatic and hydrophobic influences of aromatic ring substituents on membrane affinity and cell uptake of helical, cyclic and cell penetrating peptides. Hydrophobicity is important, but subtle changes in electrostatic surface potential, dipoles and polarizability also enhance association with phospholipid membranes and cell uptake. A combination of fluorine and sulfur substituents on an aromatic ring induces microdipoles that enhance cell uptake of 12‐residue peptide inhibitors of p53‐HDM2 interaction and of cell‐penetrating cyclic peptides. These aromatic motifs can be readily inserted into peptide sidechains to enhance their cell uptake.

Recognition of single-stranded nucleic acids by small-molecule splicing modulators

Risdiplam is the first approved small-molecule splicing modulator for the treatment of spinal muscular atrophy (SMA). Previous studies demonstrated that risdiplam analogues have two separate binding sites in exon 7 of the SMN2 pre-mRNA: (i) the 5'-splice site and (ii) an upstream purine (GA)-rich binding site. Importantly, the sequence of this GA-rich binding site significantly enhanced the potency of risdiplam analogues. In this report, we unambiguously determined that a known risdiplam analogue, SMN-C2, binds to single-stranded GA-rich RNA in a sequence-specific manner. The minimum required binding sequence for SMN-C2 was identified as GAAGGAAGG. We performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which captured spontaneous binding of a risdiplam analogue to the target nucleic acids. We uncovered, for the first time, a ligand-binding pocket formed by two sequential GAAG loop-like structures. The simulation findings were highly consistent with experimental data obtained from saturation transfer difference (STD) NMR and structure-affinity-relationship studies of the risdiplam analogues. Together, these studies illuminate us to understand the molecular basis of single-stranded purine-rich RNA recognition by small-molecule splicing modulators with an unprecedented binding mode.

Π-Stacking in Heterodimers of Propargylbenzene with (Fluoro)phenylacetylenes

The heterodimers of propargylbenzene (PrBz) with phenylacetylene (PHA) and monosubstituted fluorophenylacetylenes (FPHAs) were investigated using electronic and vibrational spectroscopic methods. The vibrational spectra in the acetylenic C-H stretching region show a marginal shift (0-4 cm-1) upon dimer formation, which suggests minimal perturbation of the acetylenic group. The M06-2X/aug-cc-pVDZ calculations indicate that the π-stacked structures are the most stable, followed by other structures. In general, structures incorporating aromatic C-H···π interactions are much higher in energy. The appearance of the spectra and the energy considerations clearly indicate the preference for the π-stacked structures. Furthermore, the observed trend in the stabilization energies for heterodimers with the three FPHAs is inversely proportional to the dipole moments of FPHAs. On the other hand, the absence of any clear trends in the electrostatic component of the interaction energy is attributed to the presence of the methylene group in PrBz.

Dipole moment enhanced π-π stacking in fluorophenylacetylenes is carried over from gas-phase dimers to crystal structures propagated through liquid like clusters

The aggregates of monofluorinated phenylacetylenes in the gas-phase, investigated using the IR-UV double resonance spectroscopic method in combination with extensive structural search and electronic structure calculations, reveal the formation of liquid-like clusters with a π-stacked dimeric core. The structural assignment based on the IR spectra in the acetylenic and aromatic C-H stretching regions suggests that, unlike the parent non-fluorinated phenylacetylene, the substitution of a F atom on the phenyl ring increases the dipole moment, leading to robustness in the formation of a ππ stacked dimer, which propagates incorporating C-Hπ_{Ar/Ac} and C-HF interactions involving both acetylenic and aromatic C-H groups. The structural evolution of fluorophenylacetylene aggregates in the gas phase shows marginal effects due to fluorine atom position on the phenyl ring, with substitution in the para-position tending towards phenylacetylene. The present study signifies that the ππ stacked dimers act as a nucleus for the growth of higher clusters to which other molecular units are added predominantly via the {Ar}_C-Hπ_{Ar} type of interaction and the dominant interactions present in the crystal structures gradually emerge with increasing cluster size. Based on these features, gas-phase clusters of fluorophenylacetylene are hypothesized as "liquid-like clusters" acting as intermediates in the generation of various polymorphic forms starting from a ππ stacked dimer as the core molecular unit.

Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. These photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates.

Switching Hydrogen Bonding to π-Stacking: The Thiophenol Dimer and Trimer

We used jet-cooled broadband rotational spectroscopy to explore the balance between π-stacking and hydrogen-bonding interactions in the self-aggregation of thiophenol. Two different isomers were detected for the thiophenol dimer, revealing dispersion-controlled π-stacked structures anchored by a long S-H···S sulfur hydrogen bond. The weak intermolecular forces allow for noticeable internal dynamics in the dimers, as tunneling splittings are observed for the global minimum. The large-amplitude motion is ascribed to a concerted inversion motion between the two rings, exchanging the roles of the proton donor and acceptor in the thiol groups. The determined torsional barrier of B₂ = 250.3 cm^-1 is consistent with theoretical predictions (290-502 cm^-1) and the monomer barrier of 277.1(3) cm^-1. For the thiophenol trimer, a symmetric top structure was assigned in the spectrum. The results highlight the relevance of substituent effects to modulate π-stacking geometries and the role of the sulfur-centered hydrogen bonds.

Dipole Moment Propels π-Stacking of Heterodimers of Fluorophenylacetylenes

Electronic and vibrational spectroscopic investigations in combination with quantum chemical calculations were carried out to probe the formation of four sets of heterodimers of phenylacetylene with 2-fluorohenylacetylene, 3-fluorophenylacetylene, 4-fluorophenylacetylene, and 2,6-difluorophenylacetylene. The interaction of phenylacetylene with fluorophenylacetylenes leads to marginal (2-9 cm^-1) red-shifts in the acetylenic C-H stretching frequencies of fluorophenylacetylenes, which suggests that constituent monomers are minimally perturbed in the heterodimer. On the other hand, the density-functional-theory-based calculations indicate that π-stacked structures outweigh other structures incorporating C-H···π and C-H···F interactions by about 8 kJ mol^-1 or more. The IR spectra in the acetylenic C-H stretching region were interpreted based on the perturbed dipole model, which suggests formation of predominantly antiparallel π-stacked structures, propelled by dipole moment. However, the energy decomposition analysis suggests that among stabilizing components dispersion dominates, while electrostatics plays a pivotal role in the formation of the π-stacked structures. Interestingly, the ability of 2-fluorophenylacetylene and 2,6-difluorophenylacetylene to π-stack differs significantly, even though both of them have almost identical dipole moments and the dipole moment propels the formation of π-stack structures. These results suggest π-stacking transcends the classical electrostatic description in terms of dipole moment.

Internal electric fields in methanol [MeOH]2-6 clusters

Water and methanol are well known solvents showing cooperative hydrogen bonding, however the differences in the hydrogen bonding pattern in water and methanol are due to the presence of the methyl group in methanol. The presence of the methyl group leads to formation of C-HO hydrogen bonds apart from the usual O-HO hydrogen bonds. The electric fields evaluated along the hydrogen bonded donor OH and CH groups reveal that the C-HO hydrogen bonds can significantly influence the structure and energetics (by about 20%) of methanol clusters. A linear Stark effect was observed on the hydrogen bonded OH groups in methanol clusters with a Stark tuning rate of 3.1 cm^-1 (MV cm^-1)^-1 as an average behaviour. Furthermore, the Stark tuning of the OH oscillators in methanol depends on their hydrogen bonding environment wherein molecules with the DAA motif show higher rates than the rest. The present work suggests that the OH group of methanol has higher sensitivity as a vibrational probe relative to the OH group of water.

Probing the role of dispersion energy on structural transformation of double-stranded xylo- and ribo-nucleic acids

The structural transformation of double-stranded octameric xyloNA and RNA were probed by modulating the dispersion energy. For the RNA, the increase and the decrease in dispersion energy lead to over-winding and unwinding of the helix. These structural transformations resemble the features observed due to the action of the topoisomerases and helicases enzymes, respectively. On the other hand, an increase in the dispersion energy has minimal effect on the structural transformation of double-strand xyloNA, whilst a decrease in the dispersion energy results in a structural transformation which happens due to the action of the helicases. The unresponsive behaviour of xyloNA to an increase in the dispersion energy is attributed to the presence of an Lpπ interaction between the oxygen atom of the xylose sugar and the adjacent nucleobase.

A liquid crucible model for aggregation of phenylacetylene in the gas phase

Structural transformation from a π-stacked dimer to an aromatic C–H⋯π trimer and a tetramer.