Electrostatics does not dictate the slip-stacked arrangement of aromatic π-π interactions.
Ontology highlight
ABSTRACT:
SUBMITTER: Carter-Fenk K
PROVIDER: S-EPMC8159364 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Aromatic-aromatic hydrogen bonds are important in many areas of chemistry, biology and materials science. In this study we have analyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-π interacting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal that these interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, the aromatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-π interactions and π-π networks play important roles in the structural stability of ILs and TNF proteins.
| S-EPMC3670127 | biostudies-literature
Project description:The recently published crystal structure of the D3 dopamine receptor shows a tightly packed region of aromatic residues on helices 5 and 6 in the space bridging the binding site and what is thought to be the origin of intracellular helical motion. This highly conserved region also makes contacts with residues on helix 3, and here we use double mutant cycle analysis and unnatural amino acid mutagenesis to probe the functional role of several residues in this region of the closely related D2 dopamine receptor. Of the eight mutant pairs examined, all show significant functional coupling (Ω > 2), with the largest coupling coefficients observed between residues on different helices, C3.36/W6.48, T3.37/S5.46, and F5.47/F6.52. Additionally, three aromatic residues examined, F5.47, Y5.48, and F5.51, show consistent trends upon progressive fluorination of the aromatic side chain. These trends are indicative of a functionally important electrostatic interaction with the face of the aromatic residue examined, which is likely attributed to aromatic-aromatic interactions between residues in this microdomain. We also propose that the previously determined fluorination trend at W6.48 is likely due to a sulfur-π interaction with the side chain of C3.36. We conclude that these residues form a tightly packed structural microdomain that connects helices 3, 5, and 6, thus forming a barrier that prevents dopamine from binding further toward the intracellular surface. Upon activation, these residues likely do not change their relative conformation, but rather act to translate agonist binding at the extracellular surface into the large intracellular movements that characterize receptor activation.
| S-EPMC3461201 | biostudies-literature
Project description:The 1:1 benzofuran-formaldehyde complex has been chosen as model system for analyzing π→π* interactions in supramolecular organizations involving heteroaromatic rings and carbonyl groups. A joint "rotational spectroscopy-quantum chemistry" strategy unveiled the dominant role of π→π* interactions in tuning the intermolecular interactions of such adduct. The exploration of the intermolecular potential energy surface led to the identification of 14 low-energy minima, with 4 stacked isomers being more stable than those linked by hydrogen bond or lone-pair→π interactions. All energy minima are separated by loose transition states, thus suggesting an effective relaxation to the global minimum under the experimental conditions. This expectation has been confirmed by the experimental detection of only one species, which was unambiguously assigned owing to the computation of accurate spectroscopic parameters and the characterization of 11 isotopologues. The large number of isotopic species opened the way to the determination of the first semi-experimental equilibrium structure for a molecular complex of such a dimension.
| S-EPMC9298890 | biostudies-literature
Project description:Thiols can engage favorably with aromatic rings in S-H/π interactions, within abiological systems and within proteins. However, the underlying bases for S-H/π interactions are not well understood. The crystal structure of Boc-l-4-thiolphenylalanine tert-butyl ester revealed crystal organization centered on the interaction of the thiol S-H with the aromatic ring of an adjacent molecule, with a through-space Hthiol···Caromatic distance of 2.71 Å, below the 2.90 Å sum of the van der Waals radii of H and C. The nature of this interaction was further examined by DFT calculations, IR spectroscopy, solid-state NMR spectroscopy, and analysis of the Cambridge Structural Database. The S-H/π interaction was found to be driven significantly by favorable molecular orbital interactions, between an aromatic π donor orbital and the S-H σ* acceptor orbital (a π → σ* interaction). For comparison, a structural analysis of O-H/π interactions and of cation/π interactions of alkali metal cations with aromatic rings was conducted. Na+ and K+ exhibit a significant preference for the centroid of the aromatic ring and distances near the sum of the van der Waals and ionic radii, as expected for predominantly electrostatic interactions. Li+ deviates substantially from Na+ and K+. The S-H/π interaction differs from classical cation/π interactions by the preferential alignment of the S-H σ* toward the ring carbons and an aromatic π orbital rather than toward the aromatic centroid. These results describe a potentially broadly applicable approach to understanding the interactions of weakly polar bonds with π systems.
| S-EPMC5890429 | biostudies-literature
Project description:In this study, charged π-electronic species are observed to develop stacking structures based on electrostatic and dispersion forces. i π- i π Interaction, defined herein, functions for the stacking structures consisting of charged π-electronic species and is in contrast to conventional π-π interaction, which mainly exhibits dispersion force, for electronically neutral π-electronic species. Establishing the concept of i π- i π interaction requires the evaluation of interionic interactions for π-electronic ion pairs. Free base (metal-free) and diamagnetic metal complexes of 5-hydroxy-10,15,20-tris(pentafluorophenyl)porphyrin were synthesized, producing π-electronic anions upon the deprotonation of the hydroxy unit. Coexisting cations in the ion pairs with porphyrin anions were introduced as the counter species of the hydroxy anion as a base for commercially available cations and as ion-exchanged species, via Na+ in the intermediate ion pairs, for synthesized π-electronic cations. Solid-state ion-pairing assemblies were constructed for the porphyrin anions in combination with aliphatic tetrabutylammonium (TBA+) and π-electronic 4,8,12-tripropyl-4,8,12-triazatriangulenium (TATA+) cations. The ordered arrangements of charged species, with the contributions of the charge-by-charge and charge-segregated modes, were observed according to the constituent charged building units. The energy decomposition analysis (EDA) of single-crystal packing structures revealed that electrostatic and dispersion forces are important factors in stabilizing the stacking of π-electronic ions. Furthermore, crystal-state absorption spectra of the ion pairs were correlated with the assembling modes. Transient absorption spectroscopy of the single crystals revealed the occurrence of photoinduced electron transfer from the π-electronic anion in the charge-segregated mode.
| S-EPMC8293984 | biostudies-literature
Project description:Non-covalent π-π interactions are central to chemical and biological processes, yet the full understanding of their origin that would unite the simplicity of empirical approaches with the accuracy of quantum calculations is still missing. Here we employ a quantum-mechanical Hamiltonian model for van der Waals interactions, to demonstrate that intermolecular electron correlation in large supramolecular complexes at equilibrium distances is appropriately described by collective charge fluctuations. We visualize these fluctuations and provide connections both to orbital-based approaches to electron correlation, as well as to the simple London pairwise picture. The reported binding energies of ten supramolecular complexes obtained from the quantum-mechanical fluctuation model joined with density functional calculations are within 5% of the reference energies calculated with the diffusion quantum Monte-Carlo method. Our analysis suggests that π-π stacking in supramolecular complexes can be characterized by strong contributions to the binding energy from delocalized, collective charge fluctuations-in contrast to complexes with other types of bonding.
| S-EPMC5309697 | biostudies-literature
Project description:The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic residues were analyzed for 511 282 pairs in 35 493 protein structures sharing less than 50% identity. Pairs with a parallel arrangement of aromatic residues made up 6.2% of all possible ones, which was twice as much as expected. Pairs with a perpendicular arrangement of aromatic residues made up 25%. We demonstrate that the most favorable arrangement was at an angle of 60° between the interacting aromatic residues. Among all possible aromatic pairs, the His-His pair was twice as frequent as expected, and the His-Phe pair was less frequent than expected. A server (CARP - Contacts of Aromatic Residues in Proteins) has been created for calculating essential structural features of interacting aromatic residues in proteins: http://bioproteom.protres.ru/arom_q_prog/.
| S-EPMC8604681 | biostudies-literature
Project description:Organic frameworks (OFs) offer a novel strategy for assembling organic semiconductors into robust networks that facilitate transport, especially the covalent organic frameworks (COFs). However, poor electrical conductivity through covalent bonds and insolubility of COFs limit their practical applications in organic electronics. It is known that the two-dimensional intralayer π∙∙∙π transfer dominates transport in organic semiconductors. However, because of extremely labile inherent features of noncovalent π∙∙∙π interaction, direct construction of robust frameworks via noncovalent π∙∙∙π interaction is a difficult task. Toward this goal, we report a robust noncovalent π∙∙∙π interaction-stacked organic framework, namely πOF, consisting of a permanent three-dimensional porous structure that is held together by pure intralayer noncovalent π∙∙∙π interactions. The elaborate porous structure, with a 1.69-nm supramaximal micropore, is composed of fully conjugated rigid aromatic tetragonal-disphenoid-shaped molecules with four identical platforms. πOF shows excellent thermostability and high recyclability and exhibits self-healing properties by which the parent porosity is recovered upon solvent annealing at room temperature. Taking advantage of the long-range π∙∙∙π interaction, we demonstrate remarkable transport properties of πOF in an organic-field-effect transistor, and the mobility displays relative superiority over the traditional COFs. These promising results position πOF in a direction toward porous and yet conductive materials for high-performance organic electronics.
| S-EPMC7456091 | biostudies-literature
Project description:When a linear aromatic molecule within a nanogap is bound only to a source electrode, and an adjacent molecule is bound only to a drain electrode, the two molecules can interact via pi-pi stacking, which allows electrons to flow from the source to the drain, via pi-pi bonds. Here we investigate the thermoelectric properties of such junctions, using mono-thiol oligo-phenylene ethynylene (OPE3)-based molecules as a model system. For molecules which are para-connected to the electrodes, we show that the Seebeck coefficient is an oscillatory function of the length L of the pi-pi overlap region and exhibits large positive and negative values. This bi-thermoelectric behavior is a result of quantum interference within the junction, which behaves like a molecular-scale Mach-Zehnder interferometer. For junctions formed from molecular monolayers sandwiched between planar electrodes, this allows both hole-like and electron-like Seebeck coefficients to be realized, by careful control of electrode separation On the other hand for meta-connected molecules, the Seebeck coefficient is insensitive to L, which may be helpful in designing resilient junctions with more stable and predictable thermoelectric properties.
| S-EPMC9082453 | biostudies-literature
Project description:Falls cause negative impacts on society and the economy. Slipping is a common initiating event for falling. Yet, individuals differ in their ability to recover from slips. Persons experiencing mild slips can accommodate the perturbation without falling, whereas severe slipping is associated with inadequate or slow pre- or post-slip control that make these individuals more prone to fall. Knowing the discrepancies between mild and severe slippers in kinematic and kinetic variables improves understanding of adverse control responsible for severe slipping. This study examined differences across these participants with respect to center of mass (COM) height, sagittal angular momentum (H), upper body kinematics, and the duration of single/double phase. Possible causality of such relationships was also studied by observing the time-lead of the deviations. Twenty healthy young adults performed walking trials in dry and slippery conditions. They were classified into mild and severe slippers based on their heel slipping speed. No inter-group differences were observed in the upper extremity kinematics. It was found that mild and severe slippers do not differ in the studied variables during normal gait; however, they do show significant differences through slipping. Compared to mild slippers, sever slippers lowered their COM height following a slip, presented higher H, and shortened their single support phase (p-value<0.05 for all). Based on the time-lead observed in H over all other variables suggests that failure to control angular momentum may influence slip severity.
| S-EPMC7067419 | biostudies-literature