Coarse-grained interaction potentials for polyaromatic hydrocarbons

Intermolecular Interactions of Pyrene and Its Oxides in Toluene Solution

In this work, the conformer-rotamer ensemble sampling tool (CREST), with the underlying semiempirical GFN2-xtb method, was used for automated geometry exploration of the homodimers of pyrene, pyrene-4,5-dione, and pyrene-4,5,9,10-tetraone, along with the heterodimer of pyrene and pyrene-4,5,9,10-tetraone. Geometries and energies of the dimers were further refined at the ωB97X-D4/def2-TZVP level of theory, both in the gas phase and in toluene solution. Computations in solution were handled using the CPCM (conductor-like polarizible continuum model) and SMD (solvation model based on density) models. Two previously unidentified pyrene-homodimer conformations were identified, and the effects of oxidation on the geometries and energies of dimerization were explored; in general, oxidation leads to stronger intermolecular interactions and decreased solubility in toluene. For selected dimers, DLPNO-CCSD(T)/cc-pVTZ/SMD(Toluene) energies were determined at the DFT geometries and illustrated the accuracy of the ωB97X-D4 approach, with an MAD of 1.47 kJ/mol.

Over What Length Scale Does an Inorganic Substrate Perturb the Structure of a Glassy Organic Semiconductor?

While the bulk structure of vapor-deposited glasses has been extensively studied, structure at buried interfaces has received little attention, despite being important for organic electronic applications. To learn about glass structure at buried interfaces, we study the structure of vapor-deposited glasses of the organic semiconductor DSA-Ph (1,4-di-[4-(N,N-diphenyl)amino]styrylbenzene) as a function of film thickness; the structure is probed with grazing incidence X-ray scattering. We deposit on silicon and gold substrates and span a film thickness range of 10-600 nm. Our experiments demonstrate that interfacial molecular packing in vapor-deposited glasses of DSA-Ph is more disordered compared to the bulk. At a deposition temperature near room temperature, we estimate ∼8 nm near the substrate can have modified molecular packing. Molecular dynamics simulations of a coarse-grained representation of DSA-Ph reveal a similar length scale. In both the simulations and the experiments, deposition temperature controls glass structure beyond this interfacial layer of a few nanometers.

Aggregation Behavior of Model Asphaltenes Revealed from Large-Scale Coarse-Grained Molecular Simulations

Fully atomistic simulations of models of asphaltenes in simple solvents have allowed the study of trends in aggregation phenomena to understand the underlying role played by molecular structure. The detail included at this scale of molecular modeling is, however, at odds with the required spatial and temporal resolution needed to fully understand asphaltene aggregation. The computational cost required to explore the relevant scales can be reduced by employing coarse-grained (CG) models, which consist of lumping a few atoms into a single segment that is characterized by effective interactions. In this work, CG force fields developed via the statistical associating fluid theory (SAFT-γ) [ Müller , E. A. ; Jackson , G. Annu. Rev. Chem. Biomol. Eng. 5 , 2014 , 405 - 427 ] equation of state (EoS) provide a reliable pathway to link the molecular description with macroscopic thermophysical data. A recent modification of the SAFT-VR EoS [ Müller , E. A. ; Mejía , A. Langmuir 33 , 2017 , 11518 - 11529 ], which allows for the parameterization of homonuclear rings, is selected as the starting point to develop CG models for polycyclic aromatic hydrocarbons. The new aromatic-core models, along with others published for simpler organic molecules, are adopted for the construction of asphaltene models by combining different chemical moieties in a group-contribution fashion. We apply the procedure to two previously reported asphaltene models and perform molecular dynamics simulations to validate the coarse-grained representation against benchmark systems of 27 asphaltenes in a pure solvent (toluene or heptane) described in a fully atomistic fashion. An excellent match between both levels of description is observed for the cluster size, radii of gyration, and relative-shape-anisotropy-factor distributions. We exploit the advantages of the CG representation by simulating systems containing up to 2000 asphaltene molecules in an explicit solvent investigating the effect of asphaltene concentration, solvent composition, and temperature on aggregation. By studying large systems facilitated by the use of CG models, we observe stable continuous distributions of molecular aggregates at conditions away from the two-phase precipitation point. As a further example application, a widely accepted interpretation of cluster-size distributions in asphaltenic systems is challenged by performing system-size tests, reversibility checks, and a time-dependence analysis. The proposed coarse-graining procedure is seen to be general and predictive and, hence, can be applied to other asphaltenic molecular structures.

Coarse-graining strategy for molecular pair interactions: A reaction coordinate study for two- and three-dimensional systems

We investigate and provide optimal sets of reaction coordinates for mixed pairs of molecules displaying polar, uniaxial, or spherical symmetry in two and three dimensions. These coordinates are non-redundant, i.e., they implicitly involve the molecules' symmetries. By tabulating pair interactions in these coordinates, resulting tables are thus minimal in length and require a minimal memory space. The intended fields of application are computer simulations of large ensembles of molecules or colloids with rather complex interactions in a fluid or liquid crystalline phase at low densities. Using effective interactions directly in the form of tables can help bridging the time and length scales without introducing errors stemming from any modeling procedure. Finally, we outline an exemplary computational methodology for gaining an effective pair potential in these coordinates, based on the Boltzmann inversion principle, by providing a step-by-step recipe.

Molecular Dynamics Simulations and their Application to Thin-film Devices

The performance of devices based on organic semiconductors strongly depends on the molecular organisation in thin films. Due to the intrinsic complexity of these systems, a combination of theoretical modelling and experimental techniques is often the key to achieve a full understanding of their inner working. Here, we introduce the modelling of organic semiconductors by means of molecular dynamics simulations. We describe the basic theoretical framework of the technique and review the most popular class of force fields used to model organic materials, paying particular attention to the peculiarities of confined systems like nano-thick films. Representative studies of the organisation of organic functional materials in thin film phases are also reviewed.

Alchemical Variations of Intermolecular Energies According to Molecular Grand-Canonical Ensemble Density Functional Theory

Molecular grand-canonical density functional theory [J. Chem. Phys. 2006, 125, 154104] is employed for the alchemical variation of intermolecular energies due to changes in the chemical composition of small molecules. We investigate the interaction of a fixed binding target, formic acid, with a restricted chemical space, corresponding to an isoelectronic 10-proton system which includes molecules such as CH4, NH3, H2O, and HF. Differential expressions involving the nuclear chemical potential are derived, numerically evaluated, tested with respect to finite difference results, and discussed regarding their suitability as gradients of the intermolecular energy with respect to compositional variations.

Organic semiconductors: impact of disorder at different timescales

The charge transport in organic materials, from molecular crystals to polymers, is determined by their degree of disorder. The dynamic disorder in ideal molecular crystals at room temperature and the static disorder in disordered polymers are just two limiting cases of the timescale of the fluctuations in the electronic Hamiltonian caused by nuclear motions. In fact, a very large number of important materials (e.g. liquid crystalline semiconductors) are actually in an intermediate regime where the disorder is neither purely static nor purely dynamic. This Minireview discusses the recent contribution of computational chemistry (molecular dynamics and quantum chemistry) to the characterization of these transport regimes and outlines the theoretical methods that can be used to relate the system characteristics to the measurable mobility.

Theoretical characterization of the structural and hole transport dynamics in liquid-crystalline phthalocyanine stacks

We present a joint molecular dynamics (MD)/kinetic Monte Carlo (KMC) study aimed at the atomistic description of charge transport in stacks of liquid-crystalline tetraalkoxy-substituted, metal-free phthalocyanines. The molecular dynamics simulations reproduce the major structural features of the mesophases, in particular, a phase transition around 340 K between the rectangular and hexagonal phases. Charge transport simulations based on a Monte Carlo algorithm show an increase by 2 orders of magnitude in the hole mobility when accounting for the rotational and translational dynamics. The results point to the formation of dynamical structural defects along the columns.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

Theory and computer simulation for the cubatic phase of cut spheres

The phase behavior of a system of hard-cut spheres has been studied using a high-order virial theory and by Monte Carlo simulation. The cut-sphere particles are disks of thickness L formed by symmetrically truncating the end caps of a sphere of diameter D . The virial theory predicts a stable nematic phase for aspect ratio LD=0.1 and a stable cubatic phase for LD=0.15-0.3 . The virial series converges rapidly on the equation of state of the isotropic and nematic phases, while for the cubatic phase the convergence is slower, but still gives good agreement with the simulation at high order. It is found that a high-order expansion (up to B8 ) is required to predict a stable cubatic phase for LD> or =0.15 , indicating the importance of many-body interactions in stabilizing this phase. Previous simulation work on this system has focused on aspect ratios LD=0.1 , 0.2, and 0.3. We expand this to include also LD=0.15 and 0.25, and we introduce a fourth-rank tensor to measure cubatic ordering. We have applied a multiparticle move which dramatically speeds the attainment of equilibrium in the nematic phase and therefore is of great benefit in the study of the isotropic-nematic phase transition. In agreement with the theory, our simulations confirm the stability of the nematic phase for LD=0.1 and the stability of the cubatic phase over the nematic for LD=0.15-0.3 . There is, however, some doubt about the stability of the cubatic phase with respect to the columnar. We have shown that the cubatic phase found on compression at LD=0.1 is definitely metastable, but the results for LD=0.2 were less conclusive.

Supramolecular routes towards liquid crystalline side-chain polymers

Supramolecular attachment of mesogenic or non-mesogenic side chains to polymer backbones can result in the formation of liquid crystalline morphologies. The various parameters that can be tuned in order to achieve these morphologies, such as the type of non-covalent bonding chemistry (hydrogen bonding, ionic bonding, metal coordination, π-π interactions), the polymeric template architecture, and the side chain structure and properties, are reviewed in what follows, with emphasis placed on the role these parameters play in the determination of the final material morphologies and properties.

The erratic emission of pyrene on gold nanoparticles

Gold nanoparticles functionalized with chromophores are known to present unpredictable fluorescence as a function of their structure. Odd-even effects, based on the number of methylene units of the chain to which the fluorophore is attached, and the nature of the anchoring group on the gold surface have, in the past, been suggested to be responsible for the behavior. Here we investigate the fluorescence processes of two newly synthesized pyrene derivatives bound to gold nanoparticles. Two structurally identical ligands, differing only in the nature of the anchoring group (a thiolate in one case and an amine in the other), were newly synthetized and attached to the gold nanoparticles. The same changes in the fluorescence properties, namely, a red spectral shift with a moderate increase of the quantum yield and a shortening of the excited-state lifetime, are observed in the two cases and ascribed to the proximity of the gold core. By comparison with the results reported for other pyrene derivatives, it has been possible to draw the conclusions that (i) the nature of the binding group does not affect the fluorescence properties of the fluorophores attached to the nanoparticle surface and (ii) much stronger fluorescence is observed in the case of pyrene separated from the gold by short alkyl chain. The unusual behavior is explained in simple terms of competing chain-chain and chromophore-chromophore interactions and by means of proper energy diagrams.

Predicting noncovalent interactions between aromatic biomolecules with London-dispersion-corrected DFT

Within the framework of Kohn-Sham density functional theory, interaction energies of hydrogen bonded and pi-pi stacked supramolecular complexes of aromatic heterocycles, nucleobase pairs, and complexes of nucleobases with the anti-cancer agent ellipticine as well as its derivatives are evaluated. Dispersion-corrected atom-centered potentials (DCACPs) are employed together with a generalized gradient approximation to the exchange correlation functional. For all systems presented, the DCACP calculations are in very good agreement with available post Hartree-Fock quantum chemical results. Estimates of 3-body contributions (<15% of the respective interaction energy) and deformation energies (5-15% of the interaction energy) are given. Based on our results, we predict a strongly bound interaction energy profile for the ellipticine intercalation process with a stabilization of nearly 40 kcal/mol (deformation energy not taken into account) when fully intercalated. The frontier orbitals of the intercalator-nucleobase complex and the corresponding non-intercalated nucleobases are investigated and show significant changes upon intercalation. The results not only offer some insights into the systems investigated but also suggest that DCACPs can serve as an effective way to achieve higher accuracy in density functional theory without incurring an unaffordable computational overhead, paving ways for more realistic studies on biomolecular complexes in the condensed phase.

Laser desorption/ionization determination of molecular weight distributions of polyaromatic carbonaceous compounds and their aggregates

Molecular weight distributions (MWDs) of model polyaromatic hydrocarbons (PAHs) and complex asphaltene samples have been investigated in laser desorption/ionization mass spectrometry (LDI-MS) experiments. Special efforts are devoted to the characterization of aggregation effects during the desorption process. It is found that non-covalent clusters of the PAHs and asphaltenes form readily in the desorbing plume. Aggregation is favoured in the experiments performed on dense samples at high laser energy and under continuous ion extraction conditions. In the absence of polar groups in the analyte molecules, the aggregation propensity correlates well with the size of the polycondensed system and with its degree of pericondensation, in qualitative agreement with previous theoretical predictions. For the polydispersed asphaltenes from two different crude oils, MWDs peaking at masses smaller than 500 amu with a high-mass tail extending up to about 3000 amu have been observed, yielding average weights around 900 amu. Such MWDs are in good agreement with previous mass spectrometric measurement, as well as with diffusion studies in solution. In addition, stable asphaltene aggregates have been detected giving rise to two broad bands in the mass spectrum corresponding to average molecular weights of 2200-3100 amu and 15,000-19,000 amu, respectively. It is concluded that the strong aggregation propensity of asphaltenes is likely to be responsible for the apparent inconsistency between the MWD for these compounds determined by different groups in independent LDI-MS experiments. The reliability of different sample preparation procedures, including solvent-free methods, is discussed, and strategies are outlined that serve to apply the potentiality of LDI mass spectrometry to the characterization of covalent and non-covalent compounds in complex carbonaceous systems.

Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules

Kohn-Sham density functional theory (KS-DFT) is nowadays the most widely used quantum chemical method for electronic structure calculations in chemistry and physics. Its further application in e.g. supramolecular chemistry or biochemistry has mainly been hampered by the inability of almost all current density functionals to describe the ubiquitous attractive long-range van der Waals (dispersion) interactions. We review here methods to overcome this defect, and describe in detail a very successful correction that is based on damped -C(6).R(-6) potentials (DFT-D). As examples we consider the non-covalent inter- and intra-molecular interactions in unsaturated organic molecules (so-called pi-pi stacking in benzenes and dyes), in biologically relevant systems (nucleic acid bases/pairs, proteins, and 'folding' models), between fluorinated molecules, between curved aromatics (corannulene and carbon nanotubes) and small molecules, and for the encapsulation of methane in water clusters. In selected cases we partition the interaction energies into the most relevant contributions from exchange-repulsion, electrostatics, and dispersion in order to provide qualitative insight into the binding character.