Conformational Effects Research Articles

PAMAM-Calix-Dendrimers: Third Generation Synthesis and Impact of Generation and Macrocyclic Core Conformation on Hemotoxicity and Calf Thymus DNA Binding

Background/Objectives: Current promising treatments for many diseases are based on the use of therapeutic nucleic acids, including DNA. However, the list of nanocarriers is limited due to their low biocompatibility, high cost, and toxicity. The design of synthetic building blocks for creating universal delivery systems for genetic material is an unsolved problem. In this work, we propose PAMAM dendrimers with rigid thiacalixarene core in various conformations, i.e., PAMAM-calix-dendrimers, as a platform for a supramolecular universal constructor for nanomedicine. Results: Third generation PAMAM dendrimers with a macrocyclic core in three conformations (cone, partial cone, and 1,3-alternate) were synthesized for the first time. The obtained dendrimers were capable of binding and compacting calf thymus DNA, whereby the binding efficiency improved with increasing generation, while the influence of the macrocyclic core was reduced. A dramatic effect of the macrocyclic core conformation on the hemolytic activity of PAMAM-calix-dendrimers was observed. Specifically, a notable reduction in hemotoxicity was associated with a decrease in compound amphiphilicity. Conclusions: We hope the results will help reduce financial and labor costs in developing new drug delivery systems based on dendrimers.

Chromatographic Determination of Permeability-Relevant Lipophilicity Facilitates Rapid Analysis of Macrocyclic Peptide Scaffolds.

Hydrocarbon-determined shake-flask measurements have demonstrated great utility for optimizing lipophilicity during early drug discovery. Alternatively, chromatographic methods confer reduced experimental error and improved handling of complex mixtures. In this study, we developed a chromatographic approach for estimating hydrocarbon-water shake-flask partition coefficients for a variety of macrocyclic peptides and other bRo5 molecules including PROTACs. The model accurately predicts experimental shake-flask measurements with high reproducibility across a wide range of lipophilicities. The chromatographic retention times revealed subtle conformational effects and correlated with the ability to sequester hydrogen bond donors in low dielectric media. Estimations of shake-flask lipophilicity from our model also accurately predicted trends in MDCK passive cell permeability for a variety of thioether-cyclized decapeptides. This method provides a convenient, high-throughput approach for measuring lipophilic permeability efficiency and predicting passive cell permeability in bRo5 compounds that is suitable for multiplexing pure compounds or investigating the properties of complex library mixtures.

Systematic Investigation on Acid-Catalyzed Truncation of N-Acylated Peptoids

Peptoids have emerged as a useful alternative to peptides. However, N-acylated peptoids have occasionally undergone truncation at the terminal peptoid unit under acidic conditions. We previously reported on the mechanistic and electronic aspects of the acid-catalyzed truncation of N-acylated peptoids. To gain further insight, we systematically investigated the conformational and electronic effects of the terminal side chains of peptoids. The n→π* interaction, based on cis/trans-amide bond conformation, is considered to be one of the determining factors. In this study, it was demonstrated that both conformational and electronic factors contribute to this unusual truncation.

Diphenylacetylene‐Incorporating Octaphyrin: A Rigid Macrocycle with Readily Separable Conformational Isomers

AbstractAn expanded carbaporphyrinoid analogue, octaphyrin(2,1,1,1,2,1,1,1), containing two rigid diphenylacetylene moieties is reported. In contrast to traditional pyrrolic macrocycles where flexible conformers coexist in dynamic equilibrium, this macrocycle exists as two separable, conformationally stable stereoisomers, denoted as 1A and 1B. The conformational effect of both conformers, as well as their protonated forms, were thoroughly studied using NMR spectroscopy, UV/Vis, and single crystal X‐ray diffraction analyses. Importantly, heating conformer 1B leads to its irreversible conversion to 1A, whereas in its protonated form, 1A ⋅ 2MSA undergoes irreversible transformation to 1B ⋅ 2MSA at lower temperatures. These temperature‐dependent features establish a foundation for developing new accumulated heat sensors, as demonstrated by the use of the present octaphyrins as a customized thermochromic indicator in steam sterilization. The present study thus underscores how the conformational rigidity of these new polypyrrolic macrocycles imparts properties that are distinct from historically flexible expanded porphyrinoids.

Platinum stabilises a molten-globule conformation of a small globular cytosolic protein SUMO1.

Proteins are generally resistant to large conformational changes under physiological conditions. Here, we show that platinum (Pt(II)), which is widely-used metal centre in cancer therapeutic drugs, binds to a cytosolic protein, small ubiquitin-like modifier 1 (SUMO1), under physiological conditions and changes its conformation to a molten globule (MG). Mass spectrometry (ICP-MS) studies confirmed stoichiometric Pt(II) binding to SUMO1. Fluorescence spectroscopy showed Tyr fluorescence quenching and increased ANS binding. Fluorescence assays on Trp-mutants indicated conformational changes and circular dichroism (CD) suggested MG formation upon Pt(II) binding. In contrast, structural homologues of SUMO1 (ubiquitin (Ubq) and SUMO2) showed no conformational changes on Pt(II) titration. Further studies compared the impact of distinct His residues in SUMO1 on Pt(II) binding and protein structure to SUMO2 and Ubq. Experiments at low pH (5.0) implicated His residues interacting with Pt(II), corroborated by the absence of conformational change in the H75L mutant of SUMO1. Pt(II)-His binding in SUMO1 unravels key molecular determinants of Pt(II)-protein interactions and their conformational consequences. SUMO1 with other SUMOylation components are shown to have enhanced expression in several cancers, hence, our study suggests a possible fate of the non-targetability of Pt(II)-based drugs on SUMOylation in cancer cells, upon interaction with SUMO1.

A-138 Implications of native protein conformation in the IgM quantification: total Ig vs HLC methods comparison

Abstract Background For IgM monoclonal gammopathies such as Waldenström Macroglobulinemia, the diagnosis, risk stratification and monitoring response to therapy is based on the detection and quantification of the secreted IgM monoclonal protein. Accurate IgM measurement is challenging due to its complex nature and the occurrence in higher polymeric structures (i.e., pentamers or hexamers), as well as heterogeneity and inherent subjectivity of the selected common methodologies. The recently developed Heavy/Light chain assay (Binding Site, part of Thermofisher Scientific) allows the separate determination of the IgM-Kappa and IgM-Lambda molecules, offering an alternative method to the serum electrophoresis (SPE) with reported higher sensitivity (Ref. Boyle E. et al, Clin Cancer Research 2016). In this study we explore the effect of the molecular structure on 3 different analytical techniques for accurate IgM measurements Methods 214 serum samples from patients (age median 63yo) under follow-up at our hospital were tested for: IgG, IgA, and IgM levels (immunoturbidimetry, either on a Beckman Coulter AU5800 analyser; Nyon, Switzerland; or a Cobas c 702 system, Roche Diagnostics); Hevylite assay (on an Optilite, Binding Site); and SPE and Immunofixation (Capillarys 3 Octa and Hydrasys 2, Sebia Inc.). The effect of the molecular conformation was evaluated through sample depolymerization with N-Acetylcysteine (NAC) according to the manufacturer’s instruction (Sebia Inc.) and IgM quantification by: tIgM (immunoturbidimetric total Ig); red-Ig (idem after NAC reduction); and, HLC-Ig (i. e. sum of the IgM-K+IgM-L heavy/light chain pair measured by Hevylite (Binding Site)). Results Total-Ig, red-Ig, and HLC-Ig returned similar results for IgG and IgA immunoglobulins (Kruskal-Wallis test, p-value > 0.05), and Passing Bablok regression analysis showed good agreement between the three methods, except for higher IgA levels. In the later, both HLC-IgA levels red-IgA values were higher than total-IgA. Regarding the IgM, PB regression revealed a significant proportional bias, with obtained values approx. 2,5x higher by red-IgM and approx. 1,4x by HLC-IgM methods than tIgM (red-IgM=-5.5+2.42*tIgM, Spearman’s r=0.995; HLC-IgM=-0,77+1.34*tIgM, Spearman’s r=0.978; red-IgM=-6.29+1.82*HLC-IgM, Spearman’s r=0.98). So, both red-IgM and HLC-IgM results are higher than total IgM. Of note, 1 sample presented antigen excess, resulting in unusually low IgM levels by tIgM but high red-IgM and high HLC-IgM levels coherent with the patient’s clinical condition. 75 samples had monoclonal protein measurable by SPE, showing good correlation with the three methods, however with greater proportional errors between measurements with other techniques Conclusions IgM molecular conformational status may affect the epitopes exposed and, therefore, available for the different assays’ recognition. Higher IgM complexes depolymerization into monomeric conformation results in higher IgM levels, which agree better with the Hevylite than with the total IgM measured previous NAC reduction, reflecting the impact of the native protein conformation in the IgM precise detection. Although also affected by the conformational status, Hevylite IgM results were closer to the reduced IgM levels than the obtained by the total IgM assay, therefore offering a sensitive assay that does not need a reduction treatment for a more accurate IgM quantification, optimizing the laboratory workflow

Exploring the Effect of Ionic Liquid Conformation on the Selective CO2 Capture of Supported Ionic Liquid-Phase Adsorbents Based on ZIFs.

The CO2 adsorption capacity and the CO2/N2 selectivity of a series of Supported Ionic Liquid-Phase adsorbents (SILPs), including the novel inversely structured SILP "Inverse SILPs", are thoroughly investigated. ZIF-8, ZIF-69 and ZIF-70 were involved as the solid matrix, while ILs, having tricyanomethanide (TCM) as an anion and alkyl-methylimidazolium of different alkyl chain lengths (C2, C6, C8) as a cation, were used as the liquid constituents of the SILPs. The ultimate target of the work was to ratify a few recently reported cases of enhanced CO2 absorptivity in ILs due to their incorporation in ZIFs and to corroborate phenomena of CO2/N2 selectivity improvements in ZIFs, due to the presence of ILs. This ambiguity originates from the vague assumption that the pores of the ZIF are filled with the IL phase, and the free pore volume of a SILP is almost zero. Yet, through the integration of theoretical predictions with N2 porosimetry analysis of an actual sample, it is suggested that a thin layer of IL covered the exterior surface of a ZIF crystal. This layer could act as an impermeable barrier for N2, inhibiting the gas molecules from reaching the empty cavities laying underneath the liquid film during porosimetry analysis. This consideration is based on the fact that the solubility of N2 in the IL is very low, and the diffusivity at 77 K is negligible. In this context, the observed result reflects an averaged adsorptivity of both the IL phase and the empty pores of the ZIF. Therefore, it is incorrect to attribute the adsorption capacity of the SILP solely to the mass of the IL that 'hypothetically' nests inside the pore cavities. In fact, the CO2 adsorption capacity of SILPs is always less than the average adsorptivity of an ideal ZIF/IL mixture, where the two phases do not interact. This reduction occurs because some ZIF pores may become inaccessible, particularly when the IL forms a layer on the pore walls, leaving only a small empty core accessible to CO2 molecules. Additionally, the IL layer masks the active sites on the ZIF's pore walls. It should also be noted that the CO2/N2 selectivity increases only when the ZIF's pores are completely filled with the IL phase. This is because ILs have a higher CO2/N2 selectivity compared to the bare ZIF.

Antecedents and Consequences of Conformity in Halal Products

This research contains a discussion of the factors that influence the intention to purchase halal products. It is hoped that the results of this research will help entrepreneurs who produce halal products that suit current needs so that they are easier to adopt. The research design that will be used is hypothesis testing, data collection using non-probability methods with purposive sampling techniques, so that the criteria for respondents is the generation that uses halal products. The data will be analyzed using a Structural Equation Model which will previously carry out Validity and Reliability prerequisite tests on the data obtained. Research results: Promotion has a positive effect on conformity and conformity has a positive effect on intention to purchase halal products. And it is proven that Promotion has a positive effect on Intention to Purchase Halal Products which is mediated by Conformity. Meanwhile, the influence of Religiosity on Conformity was found to be insignificant. And conformity also does not mediate religiosity on intention to purchase halal products.

Probing Digital Footprints and Reaching for Inherent Preferences: A Cause-Disentanglement Approach to Personalized Recommendations

This study introduces DISC (Disentangling consumers’ Inherent preferences, item Salience effect, and Conformity effect), a novel personalized recommendation approach that leverages disentangled representation learning and causal graph modeling to provide interpretable and effective recommendations. By analyzing consumer behavior across various shopping stages, DISC identifies and differentiates the inherent factors that influence purchasing decisions. DISC cuts through biases to pinpoint consumers’ inherent preferences driving purchases, empowering platforms with the ability to deliver tailored recommendations that resonate deeply with users. Through extensive experiments on real-world data sets, DISC significantly outperforms existing methods, demonstrating its superiority in both in-sample prediction and generating recommendations that align with consumers’ true interests. With its robust performance and theoretical underpinnings, DISC holds promising implications for e-commerce platforms seeking to enhance recommendation accuracy, interpretability, and user engagement.

Computational Study on the Conformational Flexibility-Mediated Intramolecular Oxidative Spirocyclization of Procyanidin B4.

Procyanidins, found widely in foods and beverages, are prone to oxidation, yet the chemical structures of their oxidation products and the mechanisms involved remain unclear. Herein, we report that the conformation of procyanidin B4 influences its oxidation products and their stereochemistry. Eight spirocyclized oxidation products were obtained from procyanidin B4 and classified as S- or R-forms based on the configuration of the spiro carbons. The ratios of S- and R-forms derived from the compact and extended rotamers of procyanidin B4, respectively, varied with the solvent. DFT calculations suggested that the four lowest-energy conformers of procyanidin B4 are diverged by interflavan bond rotation and heterocyclic ring inversion. Conformations with an axial-oriented B-ring were estimated as reactive conformations showing proximity between reaction sites on the B- and D-rings. Moreover, the extended rotamer bearing the axially oriented B-ring showed greater stabilization by noncovalent interactions (NCIs), such as OH-π interactions, compared to the counterpart of the compact rotamer. This NCI-based stabilization accounts for a higher production of the R-form despite the predominant presence of the compact rotamer in H2O. These findings highlight the conformational effects that bias the stereoselectivity of oxidative spirocyclization in procyanidin B4, advancing our understanding of procyanidin oxidation mechanisms and product stereochemistry.

Effect of the Protein Chain Conformation on the Collapse into Nanoparticles.

Protein single-chain nanoparticles can outperform synthetic nanoparticles in biomedical applications due to enhanced biocompatibility. Compared to synthetic (co)polymers, the chemical complexity of proteins challenges chain conformation control. Here, we investigate the impact of the precursor chain conformation of bovine serum albumin (BSA) on the nanoparticle structure after intramolecular cross-linking. We explore the urea concentration (denaturant), pH, salt, cross-linker length, and concentration. Small-angle neutron scattering and dynamic light scattering experiments reveal a shrinking chain conformation upon cross-linking. However, the ability to collapse depends on solvent conditions: more expanded chains collapse more, whereas proteins that are already compact barely change in size upon cross-linking. Static light scattering measurements demonstrate that binding is primarily intramolecular. The use of a shorter cross-linker does not lead to collapse of extended chains. Overall, BSA exhibits a similar behavior to that of polymer nanoparticles, which then allows to harness the precursor conformation for morphological control.

GTAM: a molecular pretraining model with geometric triangle awareness.

Molecular representation learning is pivotal for advancing deep learning applications in quantum chemistry and drug discovery. Existing methods for molecular representation learning often fall short of fully capturing the intricate interactions within chemical bonds of 2D topological graphs and the multifaceted effects of 3D geometric conformations. To overcome these challenges, we present a novel contrastive learning strategy for molecular representation learning, named Geometric Triangle Awareness Model (GTAM). This method integrates innovative molecular encoders for both 2D graphs and 3D conformations, enabling the accurate capture of geometric dependencies among edges in graph-based molecular structures. Furthermore, GTAM is bolstered by the development of two contrastive training objectives designed to facilitate the direct transfer of edge information between 2D topological graphs and 3D geometric conformations, enhancing the functionality of the molecular encoders. Through extensive evaluations on a range of 2D and 3D downstream tasks, our model has demonstrated superior performance over existing approaches. The test code and data of GTAM are available online at https://github.com/StellaHxy/GTAM.

The Joint Solvation Interaction.

The solvent-induced interactions (SIIs) between flexible solutes can be separated into two distinct components: the solvation-induced conformational effect and the joint solvation interaction (JSI). The JSI quantifies the thermodynamic effect of the solvent simultaneously accommodating the solutes, generalizing the typical notion of the hydrophobic interaction. We present a formal definition of the JSI within the framework of the mixture expansion, demonstrate that this definition is equivalent to the SII between rigid solutes, and propose a method, partially connected molecular dynamics, which allows one to compute the interaction with existing free energy algorithms. We also compare the JSI to the more natural generalization of the hydrophobic interaction, the indirect solvent-mediated interaction, and argue that JSI is a more useful quantity for studying solute binding thermodynamics. Direct calculation of the JSI may prove useful in developing our understanding of solvent effects in self-assembly, protein aggregation, and protein folding, for which the isolation of the JSI from the conformational component of the SII becomes important due to the intra-species flexibility.

Unveiling the Influence of Linkers on Conformations of Oligomeric Acceptors for High-Performance Polymer Solar Cells.

Conformational isomerism of organic photovoltaic materials has a profound impact on their molecular packing and therefore performance of polymer solar cells (PSCs). However, the conformations of oligomeric acceptors (OAs) are mostly predicted by simulations rather than experimental determinations. Herein, the stereochemical S-shaped structure of two dimeric-type acceptor molecules, V-DYIC and V-DYIC-4F, is first confirmed with different end groups (IC for V-DYIC and IC-2F for V-DYIC-4F), incorporating vinylene linkage for connecting the distinct state-of-the-art small molecule acceptor Y-segments. Through the synthetic control of fluorination sites adjacent to the vinyl-linker, S-shaped the conformation by NMR experiments is validated. Compared to the O-shaped dimer, S-shaped conformation results in enhanced lamellar order and reduced nonradiative recombination losses. The optimal acceptor, V-DYIC-4F, achieved a champion efficiency of 18.10% with the lowest energy loss of 0.556eV in its devices paired with PM6 due to their efficient carrier transport, and suppressed recombination compared to other devices, being attributed to the synergistic effect of conformation and end group fluorination. The insights gained in this work contribute valuable knowledge of both synthetic control and structural determination of OAs, providing strategic design guidelines for the future development of dimeric acceptors toward high-efficiency PSCs.

Diphenylacetylene-Incorporating Octaphyrin: A Rigid Macrocycle with Readily Separable Conformational Isomers.

An expanded carbaporphyrinoid analogue, octaphyrin(2,1,1,1,2,1,1,1), containing two rigid diphenylacetylene moieties is reported. In contrast to traditional pyrrolic macrocycles where flexible conformers coexist in dynamic equilibrium, this macrocycle exists as two separable, conformationally stable stereoisomers, denoted as 1A and 1B. The conformational effect of both conformers, as well as their protonated forms, were thoroughly studied using NMR spectroscopy, UV-Vis, and single crystal X-ray diffraction analyses. Importantly, heating conformer 1B leads to its irreversible conversion to 1A, whereas in its protonated form, 1A·2MSA undergoes irreversible transformation to 1B·2MSA at lower temperatures. These temperature-dependent features establish a foundation for developing new accumulated heat sensors, as demonstrated by the use of the present octaphyrins as a customized thermochromic indicator in steam sterilization. The present study thus underscores how the conformational rigidity of these new polypyrrolic macrocycles imparts properties that are distinct from historically flexible expanded porphyrinoids.

Modulating the Photophysical Properties of Twisted Donor-Acceptor-Donor π-Conjugated Molecules: Effect of Heteroatoms, Molecular Conformation, and Molecular Topology.

ConspectusModulating the photophysical properties of organic emitters through molecular design is a fundamental endeavor in materials science. A critical aspect of this process is the control of the excited-state energy, which is essential for the development of triplet exciton-harvesting organic emitters, such as those with thermally activated delayed fluorescence and room-temperature phosphorescence. These emitters are pivotal for developing highly efficient organic light-emitting diodes and bioimaging probes. A particularly promising class of these emitters consists of twisted donor-acceptor organic π-conjugated scaffolds. These structures facilitate a spatial separation of the frontier molecular orbitals, which is crucial for achieving a narrow singlet-triplet energy gap. This narrow gap is necessary to overcome the endothermic reverse intersystem crossing process, enhancing the efficiency of thermally activated delayed fluorescence. To precisely modulate the photophysical properties of these emitting materials, it is essential to understand the electronic structures of new donor-acceptor scaffolds, especially those influenced by heteroatoms, as well as their conformations and topologies. This understanding not only improves the efficiency of these emitters but also expands their potential applications in advance technologies.In 2014, the Takeda group made a significant breakthrough by discovering a novel method for synthesizing U-shaped diazaacenes (dibenzo[a,j]phenazine) through an oxidative skeletal rearrangement of 1,1'-binaphthalene-2,2'-diamines. This class of compounds is typically challenging to synthesize using conventional organic reactions. The resulting unique geometric and electronic structure of U-shaped diazaacenes opened new possibilities for photophysical applications. Leveraging the U-shaped structure, photoluminescent properties, and high electron affinity, we developed twisted donor-acceptor-donor compounds. These compounds exhibit efficient thermally activated delayed fluorescence, stimuli-responsive luminochromism, heavy atom-free room-temperature phosphorescence, and anion-responsive red shifts. These innovative emitters have demonstrated significant potential in various practical applications, including organic light-emitting diode devices and advanced sensing systems.In this Account, I summarize our achievements in modulating the photofunctions of dibenzo[a,j]phenazine-cored twisted donor-acceptor-donor compounds by controlling excited-state singlet-triplet energy gaps through conformational regulation. Our comprehensive studies revealed the significant impact of heteroatoms, molecular conformations, and topologies on the photophysics of these compounds. These findings highlight the importance of molecular engineering in tailoring the photophysical properties of organic donor-acceptor π-conjugated materials for specific applications. Our research has demonstrated that incorporating heteroatoms into the molecular framework effectively tunes the electronic properties and, consequently, the photophysical behavior of the compounds. Understanding the influence of heteroatoms, conformational dynamics, and molecular topology on excited-state behavior will open new avenues for next-generation optoelectronic devices and biological technologies. These advancements include ultra-low-power displays, photonic communication, and super-resolution biomedical imaging. Ultimately, our work highlights the potential of strategic molecular design in driving innovation across various fields, paving the way for the development of cutting-edge technologies that leverage the unique properties of organic emitters.

Solvent-free synthesis of polysilane-carbazole – A green route to develop fluorescent polysilanes with amplified emission characteristics via bridge intramolecular charge transfer effect

This work presents the synthesis of a new polysilane-carbazole structure (PSCB) by hydrosilylation in solvent-free conditions. For this purpose a polyhydrosilane (PSH) with a high content in methylhydrosilyl groups was mixed with 2-(((2-(9H-carbazol-9-yl)ethoxy)carbonyl)amino)ethyl methacrylate (CB) and triturated in the presence of Karstedt catalyst. The reaction proceeds smoothly in normal conditions of pressure and temperature in a dry atmosphere. The chemical structure of the resulted polymer was determined using Fourier-transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies. Gel permeation chromatography (GPC) analysis proved the completion of the addition reaction in high yields. The computational analysis reveals the electronic structures of both CB and the PSCB molecule and highlights the significance of conformational effects on electronic structure and emission properties. The carbazole moiety acts as an electron donor, while the polysilane chain serves as an acceptor, enabling an intra-molecular through bridge charge transfer. Fluorescence measurements validate the unique structure, demonstrating an amplified emission due to the cumulative effect of the polysilane chain. The polysilane-carbazole polymer holds promise for various applications, emphasizing its potential in optoelectronic devices and sensing technologies.

Some contributions to three relevant areas in organic stereochemistry during the last decade: (1) conformational effects, (2) asymmetric organocatalysis, and (3) mechanoenzymatic processes

The present Tetrahedron Report highlights salient contributions accomplished by the author's research group during the past decade in three relevant areas of organic chemistry: (1) reexamination and interpretation of conformational effects such as the anomeric and α-effect in terms of potential stereoelectronic interactions, (2) development of strategies seeking to improve the efficiency of the emblematic chiral organocatalyst (S)-proline in asymmetric organocatalysis, and (3) the successful combination of enzymatic catalysis and mechanochemical activation in the mechanoenzymatic kinetic resolution of relevant biologically active compounds. As it happens, several of these contributions were inspired by seminal contributions of Ernest L. Eliel, Dieter Seebach, Benjamin List, Tomislav Friščić, Carsten Bolm and others, and accordingly this Tetrahedron Report provides relevant examples that cover beyond the 2015–2024 decade.

Initial pyrolysis of perhydroacenaphthene conformers: A multi-scale simulation and experimental analysis

The enduring quest for a fuel that embodies both high density and superior heat sink capacity has been a long-standing goal within the scientific community. Perhydroacenaphthene (PHAN) fuels, characterized by five-membered ring structure that enhances density, also serve as hydrogen donors to inhibit coking, showcasing significant potential in fuel applications. Given their "strain-free" cyclic configuration, PHAN fuels manifest diverse conformations like chair, boat, and twist, among others, each influencing fuel properties and subsequently affecting pyrolysis process and the utilization of heat sink. In this work, leveraging the five preferred PHAN conformers substantiated by experiments, we embarked on a comprehensive investigation into their microstructures, properties, pyrolysis behavior, and initial pyrolysis mechanisms combining with molecular simulation and experimental analysis. Among them, interaction region indicator (IRI) analysis was employed to elucidate the differences in density. Upon this foundation, taking trans-trans-trans and cis-cis-cis PHAN with minimum and maximum density as models, the effects of different conformations on the initial pyrolysis reaction were explored by micro-pyrolysis system attached to an online GC-MS/FID strategy. It was found that compared to the trans-trans-trans conformation, the cis-cis-cis conformation manifested superior initial pyrolysis activity and more substantial heat sink capacity. Moreover, upon delving into the reaction mechanism and microkinetic analysis, it became evident that the favored initial reaction type of PHAN pyrolysis was H-abstraction reaction, and cis-cis-cis PHAN presented a lower barrier and a faster reaction rate than trans-trans-trans. Additionally, in conjunction with the calculation of free energy barrier and reaction heat of numerous reactions, the kinetic and thermodynamic dominances for the initial pyrolysis pathways of trans-trans-trans and cis-cis-cis PHAN were identified. Finally, utilizing intermolecular interaction energy (ΔE), independent gradient model based on Hirshfeld partition (IGMH) and Xiamen energy decomposition analysis (XEDA), the microscale justification for cis-cis-cis PHAN conformation displaying superior initial pyrolysis activity was further unveiled. This endeavors pioneer innovative pathways for the directional development and application of PHAN conformers.

Conformational Analysis of 1,3-Difluorinated Alkanes.

Fluorine substitution can have a profound impact on molecular conformation. Here, we present a detailed conformational analysis of how the 1,3-difluoropropylene motif (-CHF-CH2-CHF-) determines the conformational profiles of 1,3-difluoropropane, anti- and syn-2,4-difluoropentane, and anti- and syn-3,5-difluoroheptane. It is shown that the 1,3-difluoropropylene motif strongly influences alkane chain conformation, with a significant dependence on the polarity of the medium. The conformational effect of 1,3-fluorination is magnified upon chain extension, which contrasts with vicinal difluorination. Experimental evidence was obtained from NMR analysis, where polynomial complexity scaling simulation algorithms were necessary to enable J-coupling extraction from the strong second-order spectra, particularly for the large 16-spin systems of the difluorinated heptanes. These results improve our understanding of the conformational control toolkit for aliphatic chains, yield simple rules for conformation population analysis, and demonstrate quantum mechanical time-domain NMR simulations for liquid state systems with large numbers of strongly coupled spins.