Polyaromatic Core Research Articles

Molecular Dynamics Simulations Reveal Inhomogeneity-Enhanced Stacking of Violanthrone-78-Based Polyaromatic Compounds in n-Heptane-Toluene Mixtures.

We elucidated the effect of inhomogeneity in solutes on the aggregation of our representative polyaromatic (PA) compounds through a series of molecular dynamics simulations. Two kinds of solutes, a single type of PA compounds and a mixture of four types of PA compounds, were simulated in toluene, n-heptane, and heptol (mixture of toluene and n-heptane). The geometries of the resultant aggregates were quantified using gyradius ratios. Our results revealed that in toluene, while a single type of PA compound can only form short-cylinder-like aggregates, by having a solute mixture, parallel stacking of PA cores is enhanced, leading to the formation of one-dimensional (1D) rod-like structure. The enhanced stacking is caused by collective arrangement of the PA molecules; i.e., PA compounds of different types appear in an alternating manner in the aggregate. In addition, while the aggregated geometries of a single type of PA compounds were found to be affected by the composition of the solvents, the existence of the 1D structure formed by mixture seems to be insensitive to the solvents. On the other hand, the longest range of stacking is achieved by having a small amount of toluene ("good" solvent) in n-heptane ("bad" solvent).

Applicability of the Langmuir Equation of State for Asphaltene Adsorption at the Oil–Water Interface: Coal-Derived, Petroleum, and Synthetic Asphaltenes

In recent studies of asphaltenes from the Norwegian continental shelf at water–oil interfaces, adsorption from largely aliphatic oils appeared to be governed at early times by molecular diffusion and at later times by molecular random sequential adsorption. In addition, the interfacial tension of asphaltenes at the oil–water interface was a a unique function of interfacial coverage, and no apparent rearrangement of asphaltenes at the interface was observed within an experimental time frame of up to 12 h. Confirmation of this result was obtained by showing that high frequency elasticity is a unique function of asphaltene interfacial tension. Both interfacial tension versus coverage and elasticity versus interfacial tension data have been successfully captured by the Langmuir Equation of State (EoS), which also allows estimates of the sizes of the asphaltene polyaromatic cores to be made. The value obtained in experiments with asphaltenes from a Norwegian crude oil is 0.32 nm2/molecule, which corresponds to...

Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution.

Atomistic molecular dynamic simulations have been performed for the non-ionic chromonic liquid crystal 2,3,6,7,10,11-hexa-(1,4,7-trioxa-octyl)-triphenylene (TP6EO2M) in aqueous solution. TP6EO2M molecules consist of a central poly-aromatic core (a triphenylene ring) functionalized by six hydrophilic ethyleneoxy (EO) chains, and have a strong tendency to aggregate face-to-face into stacks even in very dilute solution. We have studied self-assembly of the molecules in the low concentration range corresponding to an isotropic solution of aggregates, using two force fields GAFF and OPLS. Our results reveal that the GAFF force field, even though it was successfully used previously for modelling of ionic chromonics, overestimates the attraction of TP6EO2M molecules in water. This results in an aggregation free energy which is too high, a reduced hydration of EO chains and, therefore, molecular self-assembly into compact disordered clusters instead of stacks. In contrast, use of the OPLS force field, leads to self-assembly into ordered stacks in agreement with earlier experimental studies of triphenylene-based chromonics. The free energy of association follows a "quasi-isodesmic" pattern, where the binding free energy of two molecules to form a dimer is of the order of 2.5 RT larger than the corresponding energy of addition of a molecule into a stack. The obtained value for the binding free energy, ΔG=-12 RT, is found to be in line with the published values for typical ionic chromonics (-7 to -12 RT), and agrees reasonably well with the experimental results for this system. The calculated interlayer distance between the molecules in a stack is 0.37 nm, which is at the top of the range found for typical chromonics (0.33-0.37 nm). We suggest that the relatively large layer spacing can be attributed to the repulsion between EO side chains.

Ultraviolet laser desorption/ionization mass spectrometry of single-core and multi-core polyaromatic hydrocarbons under variable conditions of collisional cooling: insights into the generation of molecular ions, fragments and oligomers.

The ultraviolet laser desorption/ionization of polyaromatic hydrocarbons (PAHs) has been investigated under different background pressures of an inert gas (up to 1.2 mbar of N2) in the ion source of a hybrid, orthogonal-extracting time-of-flight mass spectrometer (oTOF-MS). The study includes an ensemble of six model PAHs with isolated single polyaromatic cores and four ones with multiple cross-linked aromatic and polyaromatic cores. In combination with a weak ion extraction field, the variation of the buffer gas pressure allowed to control the degree of collisional cooling of the desorbed PAHs and, thus, to modulate their decomposition into fragments. The dominant fragmentation channels observed are related to dehydrogenation of the PAHs, in most cases through the cleavage of even numbers of C-H bonds. Breakage of C-C bonds leading to the fragmentation of rings, side chains and core linkages is also observed, in particular, at low buffer gas pressures. The precise patterns of the combined fragmentation processes vary significantly between the PAHs. The highest abundances of molecular PAH ions and cleanest mass spectra were consistently obtained at the highest buffer gas pressure of 1.2 mbar. The effective quenching of the fragmentation pathways at this elevated pressure improves the sensitivity and data interpretation for analytical applications, although the fragmentation of side chains and of bonds between (poly)aromatic cores is not completely suppressed in all cases. Moreover, these results suggest that the detected fragments are generated through thermal equilibrium processes rather than as a result of rapid photolysis. This assumption is further corroborated by a laser desorption/ionization post-source decay analysis using an axial time-of-flight MS. In line with these findings, covalent oligomers of the PAHs, which are presumably formed by association of two or more dehydrogenated fragments, are detected with higher abundances at the lower buffer gas pressures.

One-Dimensional Self-Assembly of Polyaromatic Compounds Revealed by Molecular Dynamics Simulations

A series of molecular dynamics simulations were performed on the self-assembly of polyaromatic (PA) compounds in n-heptane. These compounds possess the same PA core but systematically varied side-chain lengths. Regardless of the side-chain lengths, the simulations revealed the formation of one-dimensional (1D) self-assemblies resulting mainly from parallel stacked PA cores. The length over which the parallel stacking persists was found to be 3-5.6 nm. The 1D self-assembly was not observed for the same PA compounds in water or toluene, suggesting the importance of solvent properties in its formation. In particular, n-heptane can prevent the side chains from interfering with PA core stacking while having limited attraction with the cores, which facilitates the 1D self-assembling. These findings, revealed at the molecular level, provide insights into controlling the self-assembling process in the design of optical and electronic nanodevices.

Molecular Dynamics Investigation on the Aggregation of Violanthrone78-Based Model Asphaltenes in Toluene

In order to investigate the aggregation mechanisms of asphaltenes in toluene, a series of molecular dynamics simulations were performed on Violanthrone78-based model asphaltenes with different aliphatic/aromatic ratios. Our simulation results show that the attraction between poly-aromatic cores is the main driving force for asphaltene aggregation in toluene, and that the extent of aggregation is independent of the aliphatic/aromatic ratios. On the other hand, analysis of the aggregated structures indicates that long side chains do hinder the formation of large direct parallel stacking structures. In contrast with water as a solvent, toluene exhibits attractive interactions with both the aliphatic and aromatic regions of the asphaltenes, hence reducing the size and stability of the asphaltene aggregates. Our findings help to elucidate, at a molecular level, the different solubility behaviors of asphaltenes in toluene and in water.

Initial Partition and Aggregation of Uncharged Polyaromatic Molecules at the Oil–Water Interface: A Molecular Dynamics Simulation Study

Initial partitioning and aggregation of several uncharged polyaromatic (PA) molecules with the same polyaromatic core but different terminal moieties at oil-water interfaces from the bulk oil phase were studied by molecular dynamics simulation. The partition of the PA molecules between the bulk organic phase and oil-water interface was highly dependent on the terminal moiety structure of the PA molecules and aromaticity of the organic phase. The polarity ratio between the oil and water phases showed a significant influence on adsorption of the PA molecules at the oil-water interface. The presence of hydrophobic aromatic moieties in PA molecules hindered the adsorption process. Larger aromatic rings in PA molecules lowered the interfacial activity due to strong intermolecular π-π interactions and molecular aggregation in the bulk oil phase. The presence of a terminal carboxylic functional group on the side chain enhanced the adsorption of the PA molecules at the oil-water interface. The fused ring plane of the uncharged PA molecules was found to preferentially adsorb at the oil-water interface in a head-on or side-on orientation with the polyaromatic core staying in the nonaqueous phase (i.e., the principal plane of the molecule perpendicular to the oil-water interface). The results obtained from this study could provide a scientific direction for the design of proper chemical demulsifiers for PA molecule-mediated emulsions formed under specific process conditions of temperature, pressure, and pH.

Sensitivity of the aggregation behaviour of asphaltenes to molecular weight and structure using molecular dynamics

Asphaltenes are heavy crude oil compounds, defined as soluble in toluene and precipitating in alkanes. To understand the relation between asphaltene structure and aggregation, we perform equilibrium molecular dynamics with Large-scale Atomic and Molecular Massively Parallel Software (LAMMPS), using the atomistic force field PCFF+ in the MedeA® environment. The following three molecular models are considered: the continental model (1350 g/mol) that has a large polyaromatic core and long alkyl chains, the island model (780 g/mol) that has a smaller polyaromatic unit and shorter chains and the archipelago model (1350 g/mol) that has three polyaromatic nuclei bridged with alkyl chains. The aggregation in a given solvent is monitored by visualising solvent-free configurations over 15 ns trajectories at 350 K. Nanoaggregates are characterised by stacked polyaromatic units separated by 0.33–0.4 nm. Irreversible aggregation is found with the continental model in both solvents. Aggregation of the island model is significant in n-heptane and low in toluene. The archipelago model does not aggregate significantly. Our results confirm that the island model is a reasonable average model of asphaltenes [Headen TF, Boek ES, Skipper NT. Energy Fuels 2009;23:1220–1229]. The open structure of nanoaggregates and the limited number of stacked molecules are also in agreement with previous interpretations of experimental data [Fenistein D. et al. Langmuir 1998;14:1013–1020].

Probing the Effect of Side-Chain Length on the Aggregation of a Model Asphaltene Using Molecular Dynamics Simulations

A series of molecular dynamics simulations were performed to investigate the effect of aliphatic side-chain length on the aggregation behavior of a model asphaltene in water. We found that the extent of aggregation has a nonmonotonic relationship with the side-chain length. Asphaltene molecules with very short or very long side chains can form dense aggregates, whereas those with intermediate chain lengths cannot. Through analysis of the kinetics and driving forces of the aggregation, the role of the side chains in affecting the aggregation behavior was elucidated. Long side chains hinder the formation of parallel stacking structures of the polyaromatic cores while also favoring aggregation through hydrophobic association. The simulation results reported here can be used to propose appropriate means to reduce the extent of aggregation of asphaltene in the presence of water.

Novel discotic liquid crystal oligomers: 1,3,5-triazine-based triphenylene dimer and trimer with wide mesophase

Series of novel 1,3,5-triazine-based triphenylene oligomers 7, 10 and 12 with large bridging polyaromatic core were designed and synthesised by simple procedures in high yields. Their structures were confirmed by FTIR, 1H NMR, ESI-MS and elemental analyses. Their mesomorphic behaviours were studied by differential scanning calorimetry, polarising optical microscopy and X-ray diffraction. 1,3,5-triazine-based triphenylene monomer 7 has no mesomorphic property, but 1,3,5-triazine-based triphenylene dimer 10 and 1,3,5-triazine-based triphenylene trimer 12 possess excellent mesomorphic properties. The mesomorphic temperature range of compound 12 was as wide as 180°C. These studies indicated that the mesomorphic properties were determined by the numbers of triphenylene units. More units of triphenylene in the oligomers resulted in better mesomorphic properties.

Probing Structure–Nanoaggregation Relations of Polyaromatic Surfactants: A Molecular Dynamics Simulation and Dynamic Light Scattering Study

Four synthetic perylene bisimide-based polyaromatic (PA) surfactants with a structural or functional group difference in their attached hydrophilic/hydrophobic substituent side chains were used to probe structure-nanoaggregation relations in organic media by molecular dynamics simulations and dynamic light scattering. The results from the simulated radial distribution functions and light scattering experiments indicate that variation in the structure of side chains and polarity of functional groups leads to significant variations in molecular association, dynamics of molecular nanoaggregation and structure of nanoaggregates. The aggregates of PA surfactant molecules grow to much larger sizes in heptane than in toluene. The aromatic solvent is shown to hinder molecular association by weakening π-π stacking, demonstrating the control of molecular aggregation by tuning solvent properties. In aliphatic solvent, the aggregates formed from PA surfactants of aliphatic alkyl groups and phenylalanine derivatives as a side chain usually have a higher solvent accessible surface area to accessible volume ratio (SASA:AV) than that of tryptophan derivatives in their side chains. PA surfactants with an aliphatic functional group in both side chains does not form polyaromatic π-π stacking (T-stacking) due to its strong steric hindrance in both solvents. Depending on the nature of the side chains attached, various stacking distributions, aggregation sizes, and SASA:AV ratios were obtained. In PA surfactant nanoaggregates, all of the solvent molecules were found to be excluded from the interstices of the stacked polyaromatic cores, regardless of whether the solvent molecules are aliphatic or aromatic. Although the change in the structure of side chain substituent in polyaromatic surfactants has a negligible impact on their self-diffusivity, it can strongly influence their intermolecular interactions, leading to different aggregate diffusion coefficients.

Probing Molecular Interactions of an Asphaltene Model Compound in Organic Solvents Using a Surface Forces Apparatus (SFA)

Studies on the molecular interaction mechanisms of asphaltenes in organic solvent have not reached a widely accepted conclusion, mainly because of a poor definition of asphaltene molecules and lack of accurate information on the molecular structure. In this study, N-(1-hexylheptyl)-N′-(5-carboxylicpentyl) perylene-3,4,9,10-tetracarboxylic bisimide (C5Pe) of the polyaromatic core with a proper molecular weight and heteroatoms in its structure was used as a model compound of asphaltenes in an attempt to understand interaction mechanisms of molecular aggregation in organic solvents. A surface forces apparatus (SFA) was used to directly measure the molecular interactions of C5Pe in toluene and heptane. For the interactions between two model clay (mica) surfaces across a C5Pe-in-toluene solution, the repulsion observed between the adsorbed C5Pe molecules was shown to be of a steric origin. The force–distance profiles at short separation distances under high compression force during approaching were well-fitted with the Alexander–de Gennes (AdG) scaling theory, while the weaker repulsive forces at lower compression force regime over longer separation distances can also be fitted with the AdG model using an independent set of fitting parameters, indicating the presence of possible secondary brush structures of the C5Pe molecules in toluene. For interactions of pre-adsorbed C5Pe films (C5Pe versus mica and C5Pe versus C5Pe), no significant adhesion was detected in toluene, while strong adhesion was measured in heptane. The comparison of the results obtained with the model compound C5Pe and native asphaltenes shows that C5Pe behaves quantitatively different from the real asphaltenes in the context of contact angle and interaction force profiles. However, there are qualitative similarities in terms of intermolecular forces, indicating that the polar components in real asphaltene molecules play an important role in determining their interfacial activities.

Crystallochromy of perylene pigments: Influence of an enlarged polyaromatic core region

As demonstrated in a recent model study of several perylene pigments crystallizing in the monoclinic space group $P{2}_{1}/c$, the optical properties in the crystalline phase are determined by the interference between neutral molecular excitations and charge transfer states via electron and hole transfer. In the present work, we apply this exciton model to three further perylene compounds crystallizing in the space groups $P{2}_{1}/n$, $P\stackrel{\underline{}}{1}$, and $P{2}_{1}/c$, involving two chromophores with an enlarged polyaromatic core. In all cases, the charge transfer between stack neighbors increases the second moment of the optical response, whereas a larger conjugated core results in a red shift of the neutral excitation energy of each chromophore.

Synthesis of New Chiral Chromonic Lyotropic Liquid Crystal Based on Perylenebis(dicarboximide)

LCLCs are com-posed of plank-like molecules with polyaromatic central core and hydrophilic ionic groups at the periphery. Because of the hydrophobic nature of the aromatic central core and the hydrophilic periphery, the molecules assemble into stacks with degenerated molecular orientation in the molecular plane to form chromonic nematic (N) phase. In the N phase, the columnar aggregates align parallel to each other but show no long-range positional correlations. The variety of possible geometries of aggregations is enriched by the fact that the molecular planes can adopt different orientations with respect to the axis of the aggregates. Applications of chromonic liquid crystals are relatively unexplored. Potential applications reported for chromonic liquid crystals include the fabrication of light-harvesting devices

Natural Hydrogen Donors in Petroleum Resids

A new method of measuring the donor hydrogen concentration and reactivity relative to tetralin was devised using dehydrogenation by 2−3-dichloro-5,6-dicyano-p-benzoquinone. Petroleum resids were found to contain high concentrations of natural hydrogen donors, and more are generated during thermolysis from substituted naphthenes in the resid. In contrast to the expected low concentration, the donor hydrogen concentration in the asphaltene fraction was found to be equivalent to the concentration in the full resid. However, the donor hydrogens in asphaltenes are more reactive than in any other fraction of the resid. This requires modifying the phase-separation mechanism for coke formation and the average chemical structure of asphaltenes. Thermal conversion of resid fractions in the presence of a super reactive hydrogen donor, 1,2,3,4-tetrahydroquinoline, showed that the selectivity to distillable liquids can be increased but the formation of polyaromatic cores cannot be prevented. In addition, reactive hydrogen donors greatly reduce the thermal reaction rate by reducing the free-radical concentration. On the basis of these and previous results, methods to increase visbreaker conversion and to inhibit thermal cracking are described and the concept of an economic optimum conversion in resid hydroconversion is proposed.

Molecular Control of Macroscopic Cubic, Columnar, and Lamellar Organizations in Luminescent Lanthanide-Containing Thermotropic Liquid Crystals

The connection of lipophilic gallic acid derivatives at the 5,5'- or 6,6'-positions of the rigid 2,6-bis(1-ethyl-benzimidazol-2-yl)pyridine core provides two pro-mesogenic tridentate ligands L10 and L12, whose molecular shapes, anisometries, and directional intermolecular pi-stacking can be tuned. X-ray diffraction data in the crystalline state, combined with solution 1H NMR measurements, show that complexation with trivalent lanthanides, Ln(III), produces the neutral hemi-disklike complexes [Ln(Li)(NO3)3] (i = 10, 12), which dimerize to give the rodlike bimetallic complexes [Ln2(Li)2(NO3)6] at lower temperature. The relevant thermodynamic parameters for the latter process depend on the nature of the ligand, the size of the metal ion, and the strength of the intermolecular interactions involved in the condensed phase. These three-dimensional models obtained for the complexes in the crystals and in solution are eventually confronted with small-angle XRD profiles recorded in the intermediate thermotropic liquid crystalline phase, in which the rigidity of the packed polyaromatic cores is maintained, while the alkyl chains are molten. According to the specific geometries and nuclearities of the molecular complexes, three types of mesophases (lamellar, columnar, and cubic) can be induced, which provides a direct correlation between the microscopic arrangements and the macroscopic ordering in lanthanide-containing metallomesogens.

An atomistic technique for simulating non-covalent interactions in large ensembles of high-molecular-weight polyaromatics

Molecular modelling is a particularly useful tool for studying the behaviour of high-molecular-weight pitch components, since these very large and irregular compounds are not available in pure form for fundamental experimental studies. To date detailed computational chemistry has been carried out only on small clusters of such large discotics, while simulations of bulk phases have used simple molecular potentials (e.g. Gay–Berne) that cannot be directly related to specific molecular structure. The present paper presents a new isobaric-isothermal Monte Carlo technique for simulating large ensembles of discotic molecules based on massive summation of atomic pair potentials. The technique uses explicit description of atom locations with no adjustable potential parameters and thus allows parametric study of molecular structural features such as non-planar aliphatic rings, irregularly-shaped polyaromatic cores, and methyl groups. Here the technique is described and results presented on two model irregular PAH. The simulations show detailed features of stacking and mesophase formation as a function of temperature, and the phase behaviour is shown to be sensitive to minor perturbations in the molecular structure.

Synthesis of Conjugated Polyrotaxanes.

A series of conjugated polyrotaxane insulated molecular wires are synthesised by aqueous Suzuki polymerisation, using hydrophobic binding to promote threading of the cyclodextrin units. These polyrotaxanes have conjugated polymer cores based on poly(para-phenylene), polyfluorene, and poly(diphenylene-vinylene), threaded through 0.9-1.6 cyclodextrins per repeat unit. Bulky naphthalene-3,6-disulfonate endgroups prevent the macrocycles from slipping off the conjugated polymer chains. Dialysis experiments show that the cyclodextrins become unthreaded only if smaller stoppers are used. MALDI TOF mass spectra detect oligomers with up to ten threaded cyclodextrins, and reveal the presence of some defects that result for oxidative homo-coupling of boronic acids. Weight-average molecular weights were determined by analytical ultracentrifugation, demonstrating that step-growth polymerisation is efficient enough to achieve degrees of polymerisation up to approximately 20 repeat units (84 para-phenylenes). The fluorescence spectra of these polyrotaxanes indicate that the presence of the threaded cyclodextrin macrocycles reduces the flexibility of the conjugated polymer pi-systems. Both the solution and the solid-state photoluminescence quantum yields are enhanced upon threading of the conjugated polyaromatic cores through alpha- or beta-cyclodextrins, and the emission spectra of the polyrotaxanes are blue-shifted compared to the corresponding unthreaded polymers. The greater weight of the 0-0 transition in the emission spectra, as well as the smaller Stokes shift, indicate that the polyrotaxanes are more rigid than the unthreaded polymers.

Synthesis of conjugated polyrotaxanes.

A series of conjugated polyrotaxane insulated molecular wires are synthesised by aqueous Suzuki polymerisation, using hydrophobic binding to promote threading of the cyclodextrin units. These polyrotaxanes have conjugated polymer cores based on poly(para-phenylene), polyfluorene, and poly(diphenylene-vinylene), threaded through 0.9-1.6 cyclodextrins per repeat unit. Bulky naphthalene-3,6-disulfonate endgroups prevent the macrocycles from slipping off the conjugated polymer chains. Dialysis experiments show that the cyclodextrins become unthreaded only if smaller stoppers are used. MALDI TOF mass spectra detect oligomers with up to ten threaded cyclodextrins, and reveal the presence of some defects that result for oxidative homo-coupling of boronic acids. Weight-average molecular weights were determined by analytical ultracentrifugation, demonstrating that step-growth polymerisation is efficient enough to achieve degrees of polymerisation up to approximately 20 repeat units (84 para-phenylenes). The fluorescence spectra of these polyrotaxanes indicate that the presence of the threaded cyclodextrin macrocycles reduces the flexibility of the conjugated polymer pi-systems. Both the solution and the solid-state photoluminescence quantum yields are enhanced upon threading of the conjugated polyaromatic cores through alpha- or beta-cyclodextrins, and the emission spectra of the polyrotaxanes are blue-shifted compared to the corresponding unthreaded polymers. The greater weight of the 0-0 transition in the emission spectra, as well as the smaller Stokes shift, indicate that the polyrotaxanes are more rigid than the unthreaded polymers.

Molecular landers as probes for molecular device-metal surface interactions.

Specifically designed series of molecules (landers), comprising a central rigid polyaromatic core and several spacers that decouple the board from the metallic surface, have been synthesized. UHV-STM studies, on one hand, have shown important distortions of the molecule by interaction with the substrate. On the other hand, surface restructuring results from the presence of the molecules.