Order and Conformation of Biphenyl in Cyanobiphenyl Liquid Crystals: A Combined Atomistic Molecular Dynamics and1H NMR Study

Characterizing Counterion-Dependent Aggregation of Rhodamine B by Classical Molecular Dynamics Simulations

The aggregation in a solution of charged dyes such as Rhodamine B (RB) is significantly affected by the type of counterion, which can determine the self-assembled structure that in turn modulates the optical properties. RB aggregation can be boosted by hydrophobic and bulky fluorinated tetraphenylborate counterions, such as F5TPB, with the formation of nanoparticles whose fluorescence quantum yield (FQY) is affected by the degree of fluorination. Here, we developed a classical force field (FF) based on the standard generalized Amber parameters that allows modeling the self-assembling process of RB/F5TPB systems in water, consistent with experimental evidence. Namely, the classical MD simulations employing the re-parametrized FF reproduce the formation of nanoparticles in the RB/F5TPB system, while in the presence of iodide counterions, only RB dimeric species can be formed. Within the large, self-assembled RB/F5TPB aggregates, the occurrence of an H-type RB-RB dimer can be observed, a species that is expected to quench RB fluorescence, in agreement with the experimental data of FQY. The outcome provides atomistic details on the role of the bulky F5TPB counterion as a spacer, with the developed classical FF representing a step towards reliable modeling of dye aggregation in RB-based materials.

Control of Molecular Conformation and Crystal Packing of Biphenyl Derivatives

This Review presents a discussion of the conformation of biphenyl derivatives in different chemical environments. The interplay between aromatic stabilization and steric repulsion, normally considered to explain the conformation of the molecule, is contrasted with the interpretation provided by models not based on molecular orbitals. The electronic control of conformation by means of appropriate hydrogen substitution is discussed by examples taken from chemistry and molecular electronics. Supramolecular synthons involving biphenyl are critically analyzed in terms of the molecular conformation, crystal packing and intermolecular forces. Some directions for future research on the control of the conformation of biphenyls are also presented.

Self-assembling, structure and nonlinear optical properties of fluorescent organic nanoparticles in water

Owing to their intense emission, low toxicity and solubility in aqueous medium, fluorescent organic nanoparticles (FONs) have emerged as promising alternatives to inorganic ones for the realization of exogenous probes for bioimaging applications. However, the intimate structure of FONs in solution, as well as the role played by intermolecular interactions on their optical properties, remains challenging to study. Following a recent Second-Harmonic Scattering (SHS) investigation led by two of us [Daniel et al., ACS Photonics, 2015, 2, 1209], we report herein a computational study of the structural organization and second-order nonlinear optical (NLO) properties of FONs based on dipolar chromophores incorporating a hydrophobic triphenylamine electron-donating unit and a slightly hydrophilic aldehyde electron-withdrawing unit at their extremities. Molecular dynamics simulations of the FON formation in water are associated with quantum chemical calculations, to provide insight into the molecular aggregation process, the molecular orientation of the dipolar dyes within the nanoparticles, and the dynamical behavior of their NLO properties. Moreover, the impact of intermolecular interactions on the NLO responses of the FONs is investigated by employing the tight-binding version of the recently developed simplified time-dependent density functional theory (sTD-DFT) approach, allowing the all-atom quantum mechanics treatment of nanoparticles.

Acceleration of Liquid-Crystalline Phase Transition Simulations Using Selectively Scaled and Returned Molecular Dynamics

The molecular dynamics (MD) technique to accelerate simulation of phase transition to liquid-crystalline (LC) phases is demonstrated on the model LC system 4-octyl-4'-cyanobiphenyl (8CB) smectic A phase. Simulation of a phase transition to a smectic phase is challenging because an intrinsically long simulation time and large system size are required owing to the high order and low onset temperature. Acceleration of the simulated transition of 8CB to the smectic A phase was ultimately achieved by selectively weakening the intermolecular Lennard-Jones interaction of alkyl chains and then returning the scaled interaction to the unscaled one. The total time needed to form the smectic A phase using selectively scaled and returned molecular dynamics (ssrMD) was five times shorter than that when using unscaled MD. Formation of the smectic A phase occurred only when induced polarization from the antiparallel dipole dimer point charge was included in the simulation. The use of ssrMD presented herein is anticipated to accelerate the theoretical development of self-assembled organic materials containing both rigid and flexible moieties, including LC materials.

Stable, concentrated, biocompatible, and defect-free graphene dispersions with positive charge

The outstanding properties of graphene offer high potential for biomedical applications. In this framework, positively charged nanomaterials show better interactions with the biological environment, hence there is strong interest in the production of positively charged graphene nanosheets. Currently, production of cationic graphene is either time consuming or producing dispersions with poor stability, which strongly limit their use in the biomedical field. In this study, we made a family of new cationic pyrenes, and have used them to successfully produce water-based, highly concentrated, stable, and defect-free graphene dispersions with positive charge. The use of different pyrene derivatives as well as molecular dynamics simulations allowed us to get insights on the nanoscale interactions required to achieve efficient exfoliation and stabilisation. The cationic graphene dispersions show outstanding biocompatibility and cellular uptake as well as exceptional colloidal stability in the biological medium, making this material extremely attractive for biomedical applications.

Atomistic Mechanism of Anisotropic Heat Conduction in the Liquid Crystal 4-Heptyl-4'-cyanobiphenyl: All-Atom Molecular Dynamics

All-atom molecular dynamics simulations were performed on 4-heptyl-4'-cyanobiphenyl (7CB) to study the mechanism of heat conduction in this nematic liquid crystal atomistically. To describe 7CB properly, the AMBER-type force field was optimized for the dihedral parameter of biphenyl and the Lennard-Jones parameters. The molecular dynamics calculation using the optimized force field well reproduced the experimental values of the isotropic-nematic phase transition temperature, density, and anisotropy of the thermal conductivity. Furthermore, the contributions of convection, intramolecular interaction, and intermolecular interaction to the thermal conductivity were determined by performing thermal conductivity decomposition analysis. According to the analysis, the contributions of convection, bond stretching, and bond bending interactions were higher in the direction parallel to the nematic director than that perpendicular to the director, which is the origin of the anisotropy in the nematic phase. This result indicates that the anisotropy is caused by well-aligned covalent bonds and high mobility parallel to the director. This quantitative description of the mechanism of heat conduction of 7CB is foreseen to provide new insights toward designing highly thermally conductive liquid-crystalline materials.

Shape segregation in molecular organisation: a combined X-ray scattering and molecular dynamics study of smectic liquid crystals

Temperature-dependent X-ray scattering studies have been carried out on 4-undecyloxy-4'-cyanobiphenyl (11OCB) and 4-(12,12-dimethyltridecyloxy)-4'-cyanobiphenyl (t-Bu-11OCB) in the smectic A phase, from which their layer spacings and translational order parameters were obtained. Marked differences between the layer structures of the two compounds were demonstrated, showing that the addition of the t-Bu group results in a higher translational order parameter and wider layer spacing for t-Bu-11OCB than 11OCB. Fully atomistic MD simulations of both compounds run for >1000 ns demonstrated the spontaneous formation of smectic mesophases from isotropic starting geometries, and experimental trends in order parameters and absolute layer spacings were shown to be replicated well. Further analysis showed that both the aromatic head-groups and the alkyl tail-groups exhibit interdigitation in the simulated smectic phases of both compounds, and the difference in the layer structures between 11OCB and t-Bu-11OCB could be attributed mainly to a shape segregation effect arising from the addition of the bulky t-Bu end-group to the alkyl chain.

In Silico Measurement of Elastic Moduli of Nematic Liquid Crystals

Experiments on confined droplets of the nematic liquid crystal 5CB have questioned long-established bounds imposed on the elastic free energy of nematic systems. This elasticity, which derives from molecular alignment within nematic systems, is quantified through a set of moduli which can be difficult to measure experimentally and, in some cases, can only be probed indirectly. This is particularly true of the surfacelike saddle-splay elastic term, for which the available experimental data indicate values on the cusp of stability, often with large uncertainties. Here, we demonstrate that all nematic elastic moduli, including the saddle-splay elastic constant k_{24}, may be calculated directly from atomistic molecular simulations. Importantly, results obtained through in silico measurements of the 5CB elastic properties demonstrate unambiguously that saddle-splay elasticity alone is unable to describe the observed confined morphologies.

Validating an optimized GAFF force field for liquid crystals: TNI predictions for bent-core mesogens and the first atomistic predictions of a dark conglomerate phase

Atomistic simulations of bent core mesogens provide excellent T_NI predictions and show the formation of a dark conglomerate phase.

Nonlinear optical responses of self-assembled monolayers functionalized with indolino–oxazolidine photoswitches

The second harmonic generation responses of photoresponsive self-assembled monolayers based on indolino–oxazolidine derivatives are computed using a sequential MD/DFT approach.

Distinct alignment of benzene derivatives in stretched polystyrene and polybutylacrylate gels: Specific polymer-solute interactions

We have measured the alignment of a range of benzene derivatives in cross-linked polystyrene and poly(butyl acrylate) using a small number of residual dipolar couplings and simple geometric considerations. For apolar solutes in polystyrene and protic solutes in poly(butyl acrylate), the preferred molecular orientation does not coincide with the longest molecular axis (steric aligment). This behavior may be explained by specific π-π and hydrogen bonding interactions between solute and polymer, respectively, the latter being confirmed by molecular dynamics simulations.

Principal molecular axis and transition dipole moment orientations in liquid crystal systems: an assessment based on studies of guest anthraquinone dyes in a nematic host

Analyses of MD simulations assess different definitions of the axes along which molecules align in a nematic host, and the effects of molecular flexibility on transition dipole moment orientations.

Thermotropic liquid crystal films for biosensors and beyond

Recent results on structural properties and possible bio-sensing applications of planar liquid crystal films are reviewed.

Twist-bend nematic phases of bent-shaped biaxial molecules

How can a change in molecular structure affect the relative stability and structural properties of the twist-bend nematic phase (NTB)? Here we extend the mean-field model(1) (C. Greco, G. R. Luckhurst and A. Ferrarini, Soft Matter, 2014, 10, 9318) for bent-shaped achiral molecules, to study the influence of arm molecular biaxiality and the value of the molecule's bend angle on the relative stability of NTB. In particular we show that by controlling the biaxiality of the molecule's arms, up to four ordered phases can become stable. They involve local uniaxial and biaxial variants of NTB, together with uniaxial and biaxial nematic phases. However, a V-shaped molecule shows a stronger ability to form stable NTB than a biaxial nematic phase, where the latter phase appears in the phase diagram only for bend angles greater than 140° and for large biaxiality of the two arms.

One-pot synthesis of 4'-alkyl-4-cyanobiaryls on the basis of the terephthalonitrile dianion and neutral aromatic nitrile cross-coupling

A convenient one-pot approach to alkylcyanobiaryls is described. The method is based on biaryl cross-coupling between the sodium salt of the terephthalonitrile dianion and a neutral aromatic nitrile in liquid ammonia, and successive alkylation of the long-lived anionic intermediate with alkyl bromides. The reaction is compatible with benzonitriles that contain methyl, methoxy and phenyl groups, fluorine atoms, and a 1-cyanonaphthalene residue. The variety of ω-substituted alkyl bromides, including an extra bromine atom, a double bond, cyano and ester groups, as well as a 1,3-dioxane fragment are suitable as alkylation reagents.

Experimental and molecular dynamics studies of anthraquinone dyes in a nematic liquid-crystal host: a rationale for observed alignment trends

The experimental alignment trend of a set of anthraquinone dyes in a nematic host is rationalised by calculated molecular order parameters and transition dipole moments.