Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer.

DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.

Multidimensional Potential Energy Surfaces Resolved at the RASPT2 Level for Accurate Photoinduced Isomerization Dynamics of Azobenzene.

We have used state-of-the-art ab initio restricted active RASPT2 computations using a 16 orbitals, 18 electrons active space to produce an extended three-dimensional map of the potential energy surfaces (PESs) of the ground and first nπ* excited states of azobenzene along CNNC torsion and the two CNN bending angles, which are the most relevant coordinates for the trans-cis photoisomerization process. Through comparison with fully unconstrained optimizations performed at the same level of theory, we show that the three selected coordinates suffice to correctly describe the photoisomerization mechanism and the S1-S0 crossing seam. We also provide a map of the nonadiabatic coupling between the two states in the region where they get closer in energy. Eventually, we show that treating the two CNN bending angles as independent coordinates is fundamental to break the symmetry and couple the two electronic states. The accuracy of the S0 and S1 PESs and couplings was validated with semiclassical dynamics simulations in the reduced space of the scanned coordinates, showing results in good agreement with published full-coordinate dynamics.

Can off-centre mesogen dipoles extend the biaxial nematic range?

We have investigated the possibility of extending the stability range of the biaxial nematic phase by adding an off-centre dipole of various strengths and orientations to elongated biaxial Gay-Berne (GB) mesogens yielding a relatively narrow biaxial nematic (Nbx) phase, and a smectic (Sbx) phase when dipole-less. The effect of dipoles is not easy to predict, and our previous investigations have shown the limited benefits of having a central dipole. Here we show, employing molecular dynamics (MD) simulations, that a not too strong off-centre dipole positioned along the longest axis of the nematogen can extend the temperature range of stability of the biaxial nematic phase, also shifting it towards lower temperatures.

Can multi-biaxial mesogenic mixtures favour biaxial nematics? A computer simulation study.

Extending the range of existence of biaxial nematic phases is key to their use in applications. Here, we have investigated using extensive molecular dynamics (MD) simulations of a coarse-grained model the possible advantages of using mesogenic mixtures. We have studied the phase organisation of five thermotropic mixtures of biaxial Gay-Berne (GB) ellipsoidal particles having the same volume, but different shapes and interactions, with aspect ratios ranging from rod-like to disc-like and, choosing fractional compositions so as to model a Gaussian dispersity of shapes. The parameterisation is based on a previous GB model with biaxialities of opposite sign for steric and attractive interactions which was shown to exhibit a stable biaxial nematic phase. We found that mixing different biaxial GB particles has an overall stabilising effect on the biaxial nematic phase with respect to temperature, layering and, to some extent also demixing. The mixtures show a decrease of ordering transition temperatures, a widening of nematic temperature ranges, and the formation of smectic phases at lower temperatures.

Wetting behaviour and contact angles anisotropy of nematic nanodroplets on flat surfaces.

We have studied the wetting behaviour of liquid crystal nanodroplets deposited on a planar surface, modelling the mesogens with Gay-Berne ellipsoids and the support surface with a slab of Lennard-Jones (LJ) spherical particles whose mesogen-surface affinity can be tuned. A crystalline and an amorphous planar surface, both showing planar anchoring, have been investigated: the first is the (001) facet of a LJ fcc crystal, the second is obtained from a disordered LJ glass. In both cases we find that the deposited nanodroplet is, in general, elongated and that the contact angle changes around its contour. Simulations for the crystalline substrate show that the angle of contact turns reversibly from anisotropic to isotropic when crossing the clearing transition. As far as we know this is a novel, not yet explored effect for thermotropic liquid crystals, that we hope will stimulate experimental investigations.

On the field-induced switching of molecular organization in a biaxial nematic cell and its relaxation.

We investigate the switching of a biaxial nematic filling a flat cell with planar homogeneous anchoring using a coarse-grained molecular dynamics simulation. We have found that an aligning field applied across the film, and acting on specific molecular axes, can drive the reorientation of the secondary biaxial director up to one order of magnitude faster than that for the principal director. While the π/2 switching of the secondary director does not affect the alignment of the long molecular axes, the field-driven reorientation of the principal director proceeds via a concerted rotation of the long and transversal molecular axes. More importantly, while upon switching off a (relatively) weak or intermediate field, the biaxial nematic liquid crystal is always able to relax to the initial surface aligned director state; this is not the case when using fields above a certain threshold. In that case, while the secondary director always recovers the initial state, the principal one remains, occasionally, trapped in a nonuniform director state due to the formation of domain walls.

Supramolecular organization of functional organic materials in the bulk and at organic/organic interfaces: a modeling and computer simulation approach.

The molecular organization of functional organic materials is one of the research areas where the combination of theoretical modeling and experimental determinations is most fruitful. Here we present a brief summary of the simulation approaches used to investigate the inner structure of organic materials with semiconducting behavior, paying special attention to applications in organic photovoltaics and clarifying the often obscure jargon hindering the access of newcomers to the literature of the field. Special attention is paid to the choice of the computational "engine" (Monte Carlo or Molecular Dynamics) used to generate equilibrium configurations of the molecular system under investigation and, more importantly, to the choice of the chemical details in describing the molecular interactions. Recent literature dealing with the simulation of organic semiconductors is critically reviewed in order of increasing complexity of the system studied, from low molecular weight molecules to semiflexible polymers, including the challenging problem of determining the morphology of heterojunctions between two different materials.

Mesogen polarity effects on biaxial nematics. Centrally located dipoles.

We investigate the phase organisation of thermotropic biaxial Gay-Berne (GB) mesogens yielding a biaxial nematic (Nb) phase upon endowing them with a central point dipole. We study the effects of changing the strength and orientation of the dipole on the phase behaviour, and in particular we examine, using molecular dynamics (MD) simulations, the possibility of improving the stability of the Nb phase. After mapping the boundaries of the Nb phase, we find that the strength of the embedded dipole is the parameter with the strongest influence on the mesogenic properties, while its orientation plays a minor role. For these central dipole systems, we find that the Nb phase organisation is stable only for mesogens with relatively weak dipole moments, while it disappears if electrostatic interactions become comparable in magnitude with dispersion interactions.

Phase diagram of the uniaxial and biaxial soft-core Gay-Berne model.

Classical molecular dynamics simulations have been used to explore the phase diagrams for a family of attractive-repulsive soft-core Gay-Berne models [R. Berardi, C. Zannoni, J. S. Lintuvuori, and M. R. Wilson, J. Chem. Phys. 131, 174107 (2009)] and determine the effect of particle softness, i.e., of a moderately repulsive short-range interaction, on the order parameters and phase behaviour of model systems of uniaxial and biaxial ellipsoidal particles. We have found that isotropic, uniaxial, and biaxial nematic and smectic phases are obtained for the model. Extensive calculations of the nematic region of the phase diagram show that endowing mesogenic particles with such soft repulsive interactions affect the stability range of the nematic phases, and in the case of phase biaxiality it also shifts it to lower temperatures. For colloidal particles, stabilised by surface functionalisation, (e.g., with polymer chains), we suggest that it should be possible to tune liquid crystal behaviour to increase the range of stability of uniaxial and biaxial phases (by varying solvent quality). We calculate second virial coefficients and show that they are a useful means of characterising the change in effective softness for such systems. For thermotropic liquid crystals, the introduction of softness in the interactions between mesogens with overall biaxial shape (e.g., through appropriate conformational flexibility) could provide a pathway for the actual chemical synthesis of stable room-temperature biaxial nematics.

How does the trans-cis photoisomerization of azobenzene take place in organic solvents?

The trans-cis photoisomerization of azobenzene-containing materials is key to a number of photomechanical applications, but the actual conversion mechanism in condensed phases is still largely unknown. Herein, we study the n, pi* isomerization in a vacuum and in various solvents via a modified molecular dynamics simulation adopting an ab initio torsion-inversion force field in the ground and excited states, while allowing for electronic transitions and a stochastic decay to the fundamental state. We determine the trans-cis photoisomerization quantum yield and decay times in various solvents (n-hexane, anisole, toluene, ethanol, and ethylene glycol), and obtain results comparable with experimental ones where available. A profound difference between the isomerization mechanism in vacuum and in solution is found, with the often neglected mixed torsional-inversion pathway being the most important in solvents.

A molecular level simulation of a twisted nematic cell.

We have performed a Monte Carlo simulation of a sub-micrometric twisted nematic cell with nearly 106 particles using an off-lattice molecular model of a liquid crystal. This computer experiment is a proof of principle that molecular models can be pushed to the limit of the system sizes addressable with finite element models thus bridging the mesoscopic gap for multiscale modelling while providing a direct molecular level view of the working of the display. This approach, that allows a direct prediction of molecular organisations, properties, and responses of device systems without the requirement of prior estimate or knowledge of material properties (e.g., elastic constants), is particularly important in view of simulating materials and devices for which these quantities are not known. Results for the molecular organisation are discussed, with particular regard to its helical nature in the field-off state.

A soft-core Gay-Berne model for the simulation of liquid crystals by Hamiltonian replica exchange.

The Gay-Berne (GB) potential has proved highly successful in the simulation of liquid crystal phases, although it is fairly demanding in terms of resources for simulations of large (e.g., N>10(5)) systems, as increasingly required in applications. Here, we introduce a soft-core GB model, which exhibits both liquid crystal phase behavior and rapid equilibration. We show that the Hamiltonian replica exchange method, coupled with the newly introduced soft-core GB model, can effectively speed up the equilibration of a GB liquid crystal phase by frequent exchange of configurations between replicas, while still recovering the mesogenic properties of the standard GB potential.

Towards in silico liquid crystals. Realistic transition temperatures and physical properties for n-cyanobiphenyls via molecular dynamics simulations.

We study the important n-cyanobiphenyl (with n= 4-8) series of mesogens, using modelling and molecular dynamics simulations. We are able to obtain spontaneously ordered nematics upon cooling isotropic samples of 250 molecules. By using the united-atom force field developed herein, we show that the experimental isotropic-nematic transition temperatures are reproduced within 4 K, allowing a molecular-level interpretation of the odd-even effect along the series. Other properties, like densities, orientational order parameters and NMR residual dipolar couplings are also reproduced well, demonstrating the feasibility of predictive in silico modelling of nematics from the molecular structure.

Field response and switching times in biaxial nematics.

We study by means of virtual molecular dynamics computer experiments the response of a bulk biaxial nematic to an applied external field and, in particular, the relative speed of reorientation of the principal director axis and of the secondary one, typical of these new materials, upon a pi2 field switch. We perform the simulations setting up and integrating the equations of motion for biaxial Gay-Berne particles using quaternions and a suitable time reversible symplectic integrator. We find that switching of the secondary axis is up to an order of magnitude faster than that of the principal axis, and that under fields above a certain strength a reorganization of local domains, temporarily disrupting the nematic and biaxial ordering, rather than a collective concerted reorientation occurs.

Computer simulations of biaxial nematics.

Biaxial nematic (N(b)) liquid crystals are a fascinating condensed matter phase that has baffled, for more than thirty years, scientists engaged in the challenge of demonstrating its actual existence, and which has only recently been experimentally found. During this period computer simulations of model N(b) have played an important role, both in providing the basic physical properties to be expected from these systems, and in giving clues about the molecular features essential for the thermodynamic stability of N(b) phases. However, simulation studies are expected to be even more crucial in the future for unravelling the structural features of biaxial mesogens at the molecular level, and for helping in the design and optimization of devices towards the technological deployment of N(b) materials. This review article gives an overview of the simulation work performed so far, and relying on the recent experimental findings, focuses on the still unanswered questions which will determine the future challenges in the field.

A chirality index for investigating protein secondary structures and their time evolution.

We propose a methodology for the description of the secondary structure of proteins, based on assigning a chirality parameter to short aminoacid sequences according to their arrangement in space at a certain time. We validated the method on ideal and crystalline structures, showing that it can assign secondary structures and that this assignment is robust with respect to random conformational perturbations. From the values of the index and its pattern along a sequence it is possible to recognize many structural motifs of a protein, and in particular poly-L-proline II left-handed helices, often not detected by secondary structure assignment algorithms. Assigning an instantaneous chirality index to the fragments also allows the dynamics to be studied. With this purpose, molecular dynamics simulations were carried out in water for selected hemoglobin (110 ns) and immunoglobulin antigen fragments (50 ns), showing the capability of the chiral index in identifying the stable secondary structure elements, as well as in following their time evolution and conformational changes during the trajectory.

Core charge distribution and self assembly of columnar phases: the case of triphenylenes and azatriphenylenes.

BACKGROUND: The relation between the structure of discotic molecules and columnar properties, a crucial point for the realization of new advanced materials, is still largely unknown. A paradigmatic case is that hexa-alkyl-thio substituted triphenylenes present mesogenic behavior while the corresponding azatriphenylenes, similar in shape and chemical structure, but with a different core charge distribution, do not form any liquid crystalline mesophase. This study is aimed at investigating, with the help of computer simulations techniques, the effects on phase behaviour of changes of the charge distribution in the discotic core. RESULTS: We described the shape and the pair, dispersive and electrostatic, interactions of hexa alkyl triphenylenes by uniaxial Gay-Berne discs with embedded point charges. Gay-Berne parameters were deduced by fitting the dispersive energies obtained from an atomistic molecular dynamics simulation of a small sample of hexa-octyl-thio triphenylene molecules in columnar phase, while a genetic algorithm was used to get a minimal set of point charges that properly reproduces the ab anitio electrostatic potential. We performed Monte Carlo simulations of three molecular models: the pure Gay-Berne disc, used as a reference, the Gay-Berne disc with hexa-thio triphenylene point charges, the Gay-Berne disc with hexa-thio azatriphenylene point charges. The phase diagram of the pure model evidences a rich polymorphism, with isotropic, columnar and crystalline phases at low pressure, and the appearance of nematic phase at higher pressure. CONCLUSION: We found that the intermolecular electrostatic potential among the cores is fundamental in sta-bilizing/destabilizing columnar phases; in particular the triphenylene charge distribution stabilizes the columnar structure, while the azatriphenylene distribution suppresses its formation in favor of the nematic phase. We believe the present model could be successfully employed as the basis for coarse-grained level simulations of a wider class of triphenylene derivatives.

A computer simulation study of the formation of liquid crystal nanodroplets from a homogeneous solution.

The aggregation of liquid crystal nanodroplets from a homogeneous solution is an important but not well understood step in the preparation of various advanced photonic materials. Here, the authors performed molecular dynamics computer simulations of the formation of liquid crystalline nanodroplets, starting from an isotropic and uniform binary solution of spherical Lennard-Jones (solvent) and elongated ellipsoidal Gay-Berne (solute) rigid particles in low (<10%) concentration. They studied the dynamics of demixing and the mesogen ordering process and characterized the resulting nanodroplets assessing the effect of temperature, composition, and specific solute-solvent interaction on the morphology, structure, and anisotropy. They find that the specific solute-solvent interaction, composition, and temperature can be adjusted to tune the nanodroplet growth and size.

A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.

Liquid crystal phases formed by bent-shaped (or "banana") molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.

Effect of nanoconfinement on liquid-crystal polymer chains.

We apply a Monte Carlo polymerization model for Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] monomers that we have recently introduced [J. Chem. Phys. 121, 9123 (2004)] to investigate with computer simulations the effects of nanoconfinement and anchoring type on the structure of the main-chain liquid-crystal polymers formed in thin films, in the presence of several types of surface alignment: parallel to the interface (random and uniform) or perpendicular to it (homeotropic). We perform first a study of the confined monomers and then we examine the features of the polymer chains obtained from an isotropic or nematic sample. We find a significant effect of the anchoring conditions on the characteristics of the chains and particularly striking differences between planar and homeotropic boundaries. Furthermore, our results indicate that the choice of different anchorings could be used to tune the linearity and degree of polymerization of the chains.