Polyaromatic Core Research Articles

Homolytic Versus Heterolytic Bond Breaking in Functionalized [R-C20 H10 ]+ Systems.

The comprehensive theoretical investigation of stability of functionalized corannulene cations [R-C20 H10 ]+ with respect to two alternative bond-breaking mechanisms, namely, homolytic or radical ([R-C20 H10 ]+ → R• + C20 H10 +• ) and heterolytic or cationic ([R-C20 H10 ]+ → R+ + C20 H10 ), was accomplished. The special focus was on the influence of the nature of R-group on the energetics of the bond cleavage. Detailed study of energetics of both mechanisms has revealed that the systems with small alkyl groups such as methyl tend to undergo bond breaking in accordance with homolytic mechanism. Subsequent elongation of the chain of the R-group resulted in shifting the paradigm, making heterolytic path more energetically favorable. Subsequent analysis of different components of the bonding between R-group and corannulene polyaromatic core helped to shed light on trends observed. In both mechanisms, the covalent contribution was found to be dominating, whereas ionic part contributes ~25-27%. Two leading components of ΔEorb , C20 H10 → R and R → C20 H10 , were identified with NOCV-EDA approach. While the homolytic pathway is best described as R → C20 H10 process, the heterolytic mechanism shows domination of the C20 H10 → R term. Surprisingly, the preparation energy (ΔEprep ) was identified as a key player in stability tendencies found. In other words, the relative stability of corresponding molecular fragments (here R-groups as the corannulene fragment remains the same for all systems) in their cationic or radical forms determine the preference given to a specific bond breaking path and, as consequence, the total stability of target functionalized cations. These conclusions were further confirmed by extending a set of R-groups to conjugated (allyl, phenyl), bulky (iPr, tBu), β-silyl (CH2 SiH3 , CH2 SiMe3 ), and benzyl (CH2 Ph) groups. © 2019 Wiley Periodicals, Inc.

Absorption spectroscopy to determine the extent and mechanisms of aging in bitumen and asphaltenes

Recycling of petroleum bitumen used in road and roofing shingle is widespread, and in many cases the recycled content includes bitumen that has already endured multiple consecutive cycles of service life, and their aging level varies significantly. Therefore, there is a need to accurately determine aging level for each recovered bitumen based on fundamental measures established to track physio-chemical changes that occur during progressive aging. This study examines effects of progressive aging in bitumen and introduces aging indicators based on absorption spectroscopy. Bitumen samples were exposed to accelerated aging in a pressure aging vessel (PAV) and were examined by UV–vis absorption and Fourier transform infrared spectroscopy. Absorption spectroscopy results not only showed carbonyl content consistently increased with aging time, but also revealed other distinct chemical changes such as loss of saturated hydrocarbons, followed by carbonation and then degradation of the poly-aromatic cores of asphaltenes and resins with extended aging. As such absorption spectroscopy deemed to be useful to determine extent of aging resembling multiple periods of service life for bitumen.

Alkyloxy modified pyrene fluorophores with tunable photophysical and crystalline properties

Alkyloxy modified 4,5,9,10-tetrasubstituted pyrenes display tunable photophysical and crystalline properties depending on the alkyl chains attached at the polyaromatic core.

Understanding Adsorption of Violanthrone-79 as a Model Asphaltene Compound on Quartz Surface Using Molecular Dynamics Simulations

A series of molecular dynamics simulations were performed to investigate the adsorption of violanthrone-79 (VO-79) as a model asphaltene compound on quartz surface in different organic solvents (n-heptane, toluene, and heptol with three different n-heptane/toluene volume ratios). Our simulations demonstrated that the type of solvent had a great impact on the kinetics of adsorption, such as the adsorption rate and final adsorption amount. However, the equilibrium modes of adsorption were similar: both monomer and aggregate adsorptions were observed regardless of the n-heptane and toluene contents. With monomer adsorption, the polyaromatic core (PAC) of VO-79 was merely parallel to the surface, whereas the PACs showed two types of orientations in aggregate adsorption—parallel and slant—with the majority of them slant to the surface, maintaining π–π stacking between neighboring PACs. Energetic analyses showed that the adsorption was driven primarily by van der Waals forces, accompanied by electrostatic inter...

Probing the Effect of Salt on Asphaltene Aggregation in Aqueous Solutions Using Molecular Dynamics Simulations

The presence of salts in different processes of oil production has attracted wide attention because of its effects on asphaltene aggregation, stability, interactions of emulsions, etc. In this work, molecular dynamics simulations were employed to study the effect of salts on aggregation of model asphaltenes. Four types of polyaromatic compounds possessing key structural features of continental-type asphaltenes were dispersed into NaCl solutions of different concentrations. These models have the same polyaromatic core but different lengths for the side chains. In the two models with relatively long side chains, the hydrophobic association among side chains is the main driving force for aggregation. The effect of salt on aggregation is therefore closely tied to its influence on the hydrophobic interaction: the salt ions promote the hydrophobic interaction at a low salt concentration while suppressing it at a high salt concentration. For the model with an intermediate side chain length, the hydrophobic interaction between side chains becomes less dominant and the salt has mutual influences on the core–core, chain–chain, and core–chain interactions. For the model with the shortest side chains, although the core–core and core–chain interactions are more important, the side chains still play a role in aggregation when the salt is present. Our results provide new insights into the fundamental understanding of the influence of salts on the aggregation and interaction behaviors of polyaromatic compounds in an aqueous environment.

Coarse-Grained Molecular Simulation and Nonlinear Manifold Learning of Archipelago Asphaltene Aggregation and Folding.

Asphaltenes constitute the heaviest aromatic component of crude oil. The myriad of asphaltene molecules falls largely into two conceptual classes: continental-possessing a single polyaromatic core-and archipelago-possessing multiple polyaromatic cores linked by alkyl chains. In this work, we study the influence of molecular architecture upon aggregation behavior and molecular folding of prototypical archipelago asphaltenes using coarse-grained molecular dynamics simulation and nonlinear manifold learning. The mechanistic details of aggregation depend sensitively on the molecular structure. Molecules possessing three polyaromatic cores show a higher aggregation propensity than those with two, and linear archipelago architectures more readily form a fractal network than ring topologies, although the resulting aggregates are more susceptible to disruption by chemical dispersants. The Yen-Mullins hierarchy of self-assembled aggregates is attenuated at high asphaltene mass fractions because of the dominance of promiscuous parallel stacking interactions within a percolating network rather than the formation of rodlike nanoaggregates and nanoaggregate clusters. The resulting spanning porous network possesses a fractal dimension of 1.0 on short length scales and 2.0 on long length scales regardless of the archipelago architecture. The incompatibility of the observed assembly behavior with the Yen-Mullins hierarchy lends support that high-molecular weight archipelago architectures do not occur at significant levels in natural crude oils. Low-dimensional free energy surfaces discovered by nonlinear dimensionality reduction reveal a rich diversity of metastable configurations and folding behavior reminiscent of protein folding and inform how intramolecular structures can be modulated by controlling asphaltene mass fraction and dispersant concentration.

The expansive library of jadomycins

The jadomycin family of natural products was discovered from Streptomyces venezuelae ISP5230 in the 1990s. Subsequent identification of the biosynthetic gene cluster along with synthetic efforts established that incorporation of an amino acid into the polyaromatic angucycline core occurs non-enzymatically. Over two decades, the precursor-directed biosynthetic potential of the jadomycins has been heavily exploited, generating a library exceeding 70 compounds. This review compiles the jadomycins that have been isolated and characterized to date; these include jadomycins incorporating proteinogenic and non-proteinogenic amino acids, semi-synthetic derivatives, biosynthetic shunt products, compounds isolated in structural gene deletion studies, and deoxysugar sugar variant jadomycins produced by deletion or heterologous expression of sugar biosynthetic genes.

Redox-active, pyrene-based pristine porous organic polymers for efficient energy storage with exceptional cyclic stability.

A novel class of pyrene-based conjugated porous organic polymers having an N-containing network was developed by employing Buchwald-Hartwig coupling for supercapacitor energy storage. The pristine polymer was found to exhibit a specific capacitance of 456 F g-1 at 0.5 A g-1 current density with excellent long-term cyclic stability.

Oxidation of Polynuclear Aromatic Hydrocarbons using Ruthenium‐Ion‐Catalyzed Oxidation: The Role of Aromatic Ring Number in Reaction Kinetics and Product Distribution

Oxidation of aromatic hydrocarbons with differing numbers of fused aromatic rings (2-5), have been studied in two solvent environments (monophasic and biphasic) using ruthenium-ion-catalyzed oxidation (RICO). RICO reduces the aromaticity of the polyaromatic core of the molecule in a controlled manner by selective oxidative ring opening. Moreover, the nature of the solvent system determines the product type and distribution, for molecules with more than two aromatic rings. Competitive oxidation between substrates with different numbers of aromatic rings has been studied in detail. It was found that the rate of polyaromatic hydrocarbon oxidation increases with the number of fused aromatic rings. A similar trend was also identified for alkylated aromatic hydrocarbons. The proof-of-concept investigation provides new insight into selective oxidation chemistry for upgrading of polyaromatic molecules.

NMR Characterization of Asphaltene Derived from Residual Oils and Their Thermal Decomposition

The main objective of this work is to determine the effect of thermal cracking on asphaltene molecular structure by using nuclear magnetic resonance (NMR). The NMR is used to identify and quantify the structural parameters and the functional groups, which subsequently helped in deriving a hypothetical average structure for the asphaltene molecules. The NMR analysis revealed a number of valuable findings and developed a better understanding about the nature of structural changes that asphaltene molecules undergo during the thermal cracking of vacuum residues (VRs). For instance, the polyaromatic structure of asphaltene in the parent VRs consists of peri-condensed cores interlinked through aliphatic bridges. This peri-condensed polyaromatic core converts to cata-condensed polyaromatic as the reaction severity increases. The NMR analysis confirmed that the observed reduction in the average molecular weight of asphaltene molecules, as reaction severity increases, is mainly due to cracking of the saturated par...

Interactions of Polyaromatic Compounds. Part 1: Nanoaggregation Probed by Electrospray Ionization Mass Spectrometry and Molecular Dynamics Simulation

Nanoaggregation of three synthetic polyaromatic compounds, N-(1-hexylhepyl)-N′-(5-carboxylicpentyl)-perylene-3,4,9,10-tetracarboxylicbisimide (C5Pe), N-(1-undecyldodecyl)-N′-(5-carboxylicpentyl)-perylene-3,4,9,10-tetracarboxylbisimide (C5PeC11), and N,N′-bis(1-undecyldodecyl)perylene-3,4,9,10-tetracarboxylbisimide (BisAC11), individually or in their binary mixtures was studied under various solution conditions using electrospray ionization mass spectrometry (ESI–MS) and molecular dynamics (MD) simulation. The results from ESI–MS showed a significant enhancement in nanoaggregation of each individual component by increasing their concentration or heptane addition to toluene. Mixing a polyaromatic compound of longer aliphatic chain with a shorter chain polyaromatic compound in a given solvent was found to significantly reduce the apparent average nanoaggregation number. Replacing the −COOH group with an aliphatic group induced further steric hindrance to nanoaggregation of polyaromatic cores in the mixture. ...

Effects of the asphaltene structure and the tetralin/heptane solvent ratio on the size and shape of asphaltene aggregates

Asphaltene molecules, which consist of differently hydrogenated polyaromatic cores grafted with side alkyl chains of different sizes and grafting densities, were simulated with a solvent mixture of heptane and tetralin using coarse-grained force fields. Starting with the initial configuration of randomly distributed asphaltene molecules and solvents, the asphaltene molecules aggregate because of the attractive force between their polyaromatic cores, but their sizes and shapes differ. The average aggregate size decreases with an increase in the hydrogenated polycyclic core, side-chain length, and tetralin concentration, which agree with experimental observations in the hydrocracking process. The number of side chains also influences the aggregate size but only in the presence of tetralin. In particular, the effect of tetralin addition occurs more significantly for asphaltene molecules with more side chains because side chains sterically block the intermolecular interactions between polyaromatic cores, which makes it easier for the aromatic ring of tetralin to bind to the polyaromatic core of asphaltene. These steric effects of side chains yield different shapes of aggregates, showing parallel stacking (face-to-face) for aromatic cores with many side chains, and T-shape (edge-to-face) or offset-parallel stacking for those with fewer side chains. These findings agree with the experimental observation regarding the effect of tetralin on the solubility of asphaltene, and indicate that the extent of the tetralin effect depends on the number of side alkyl chains, implying that tetralin solvents need to be added with consideration for the structural change of asphaltene under hydrogenation or dealkylation conditions.

Molecular dynamics on the self-assembly of mesogenic graphene precursors

We characterize the spontaneous aggregation of Disodium Cromoglycate (DSCG) in the isotropic phase of aqueous solutions, which is an archetypical mesogenic precursor for the supramolecular synthesis of graphenic carbons, using molecular dynamics simulations and thermodynamic scaling. DSCG belongs to a broader family of mesogenic precursors called lyotropic chromonic liquid crystals (LCLC). Previously reported experimental self-assembly features were quantitatively reproduced using a full atomistic representation. We find that the formation of hydrogen bonds between solvent water and mesogenic molecules strongly contributes to the self-assembly, a new discovery in LCLC self-assembly. We propose that aggregation is energetically driven by entropic forces which favor the formation of π-π interactions within mesogens' polyaromatic cores by reorienting DSCG hydrophilic groups towards solvent molecules. We carried out different quantitative characterizations that support this mechanism, such as radial distribution function and hydrogen bond distribution analysis. Furthermore, conformation stability calculations were studied using metadynamics sampling technique. These results provide a significant contribution to the ongoing understanding of the self-assembly of LCLC required for the characterization and synthesis of highly ordered supramolecular graphenic materials.

NMR Structure of a Triangulenium‐Based Long‐Lived Fluorescence Probe Bound to a G‐Quadruplex

AbstractAn NMR structural study of the interaction between a small‐molecule optical probe (DAOTA‐M2) and a G‐quadruplex from the promoter region of the c‐myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR‐restrained structural calculations show that binding of DAOTA‐M2 occurs mainly through π–π stacking between the polyaromatic core of the ligand and guanine residues of the outer G‐quartets. Interestingly, the binding affinities of DAOTA‐M2 differ by a factor of two for the outer G‐quartets of the unimolecular parallel G‐quadruplex under study. Unrestrained MD calculations indicate that DAOTA‐M2 displays significant dynamic behavior when stacked on a G‐quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G‐quadruplexes.

NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex.

An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through π-π stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.

Self-Accumulation of Uncharged Polyaromatic Surfactants at Crude Oil–Water Interface: A Mesoscopic DPD Study

The dissipative particle dynamics (DPD) technique was applied to study the behavior of several uncharged perylene bisimide-based polyaromatic surfactant (PAS) molecules, with the same polyaromatic core but with different terminal functional types (TP, C5Pe, PAP, and PCH) at the crude oil–water interface. We considered the SARA crude oil model with Persian Gulf oil field composition, which includes saturates, 59%; aromatics, 28.5%; resins, 9.7%; and asphaltenes, 2.8% at two temperatures 298 and 363 K. The DPD interaction parameters for the bead pairs needed in the DPD simulations were evaluated by using the well-known correlation equation, where the required Flory–Huggins interaction parameter in this equation was calculated by the blend methodology model. The results indicated that the C5Pe terminal functional type of PAS is absorbed more effectively on the water droplet interface in the crude oil system and can reduce the interfacial tension (IFT) to facilitate the oil–water separation. The results of th...

Investigation of the Effect of Sulfur Heteroatom on Asphaltene Aggregation

We present molecular dynamics simulations (MDS) for interpreting the molecular aggregation of four different asphaltene molecular models. These simulations are based on recent small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) experiments from Eyssautier and co-workers [Eyssautier, J.; Levitz, P.; Espinat, D.; Jestin, J.; Gummel, J.; Grillo, I.; Barre, L. Insight into asphaltene nanoaggregate structure inferred by small angle neutron and X-ray scattering. J. Phys. Chem. B 2011, 115 (21), 6827−6837, 10.1021/jp111468d], which proposed a discoidal asphaltene nanoaggregate structure of 0.67 nm height and its chemical composition. Basically, we have investigated the sulfur atom position in the asphaltene structure. π–π is the main type of contact, and it seems to be responsible for the parallel orientation of molecules. This geometry is also corroborated by the cosine of angles between the polyaromatic cores. However, the polar side chain is also important to the aggregation, because...

Role of Naphthenic Acids in Controlling Self-Aggregation of a Polyaromatic Compound in Toluene.

In this work, a series of molecular dynamics simulations were performed to investigate the effect of naphthenic acids (NAs) in early stage self-assembly of polyaromatic (PA) molecules in toluene. By exploiting NA molecules of the same polar functional group but different aliphatic/cycloaliphatic nonpolar tails, it was found that irrespective of the presence of the NA molecules in the system, the dominant mode of π-π stacking is a twisted, offset parallel stacking of a slightly larger overlapping area. Unlike large NA molecules, the presence of small NA molecules enhanced the number of π-π stacked PA molecules by suppressing the hydrogen bonding interactions among the PA molecules. Smaller NA molecules were found to have a higher tendency to associate with PA molecules than larger NA molecules. Moreover, the size and distribution of π-π stacking structures were affected to different degrees by changing the size and structural features of the NA molecules in the system. It was further revealed that the association between NA and PA molecules, mainly through hydrogen bonding, creates a favorable local environment for the overlap of PA cores (i.e., π-π stacking growth) by depressing the hydrogen bonding between PA molecules, which results in the removal of some toluene molecules from the vicinity of the PA molecules.

Structure-Resistance Relationships: Interrogating Antiseptic Resistance in Bacteria with Multicationic Quaternary Ammonium Dyes.

Bacterial resistance toward commonly used biocides is a widespread yet underappreciated problem, one which needs not only a deeper understanding of the mechanisms by which resistance proliferates, but also means for mitigation. To advance our understanding of this issue, we recognized a polyaromatic structural core analogous to activators of QacR, a negative transcriptional regulator of the efflux pump QacA, and envisioned a series of quaternary ammonium compounds (QACs) based on this motif. Using commercially available dye scaffolds, we synthesized and evaluated the antimicrobial activity of 52 novel QACs bearing 1-3 quaternary ammonium centers. Striking differences in antimicrobial activity against bacteria bearing QAC resistance genes have been observed, with up to a 125-fold increase in minimum inhibitory concentration (MIC) for select structures against bacteria known to bear efflux pumps. Based on these findings, general trends in structure-resistance relationships have been identified, laying the groundwork for future mechanistic studies.

Diruthenium Complexes with Bridging Diethynyl Polyaromatic Ligands: Synthesis, Spectroelectrochemistry, and Theoretical Calculations

This work describes syntheses and electrochemical, spectroscopic, and bonding properties in a new series of dinuclear ruthenium(II) complexes bridged by polyaromatic (biphenyl, fluorene, phenanthrene, and pyrene) alkynyl ligands. Longitudinal expansion of the π-conjugated polyaromatic core of the bridging ligands caused a reduced potential difference between the anodic steps and reinforced their bridge-localized nature, as evidenced by UV/vis/near-IR and IR spectroelectrochemical data combined with DFT and TDDFT calculations. Importantly, the intricate multiple IR ν(C≡C) absorption bands for the singly oxidized states imply a thermal population of a range of conformers (rotamers) with distinct electronic character. This behavior was demonstrated with more accurate DFT calculations of selected nontruncated 1e– oxidized complexes in three different conformations. The combined experimental and theoretical data reveal that thermally populated rotamers featuring various mutual orientations of the ligated metal...