Molecular dynamics of a model anisotropic system

MOLC. A reversible coarse grained approach using anisotropic beads for the modelling of organic functional materials

We describe the development and implementation of a coarse grained (CG) modelling approach where complex organic molecules, and particularly the π-conjugated ones often employed in organic electronics, are modelled in terms of connected sets of attractive-repulsive biaxial Gay-Berne ellipsoidal beads. The CG model is aimed at reproducing realistically large scale morphologies (e.g. up to 100 nm thick films) for the materials involved, while being able to generate, with a back-mapping procedure, atomistic coordinates suitable, with limited effort, to be applied for charge transport calculations. Detailed methodology and an application to the common hole transporter material α-NPD are provided.

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 (N_bx) phase, and a smectic (S_bx) 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

A mixture of mesogens with different anisotropies favours the biaxial nematic phase.

Molecular dynamics simulations and NMR spectroscopy studies of trehalose-lipid bilayer systems

The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

Molecular dynamics simulations of membranes composed of glycolipids and phospholipids

Lipid membranes composed of 1,2-di-(9Z,12Z,15Z)-octadecatrienoyl-3-O-β-D-galactosyl-sn-glycerol or monogalactosyldiacylglycerol (MGDG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were studied by means of molecular dynamics (MD) computer simulations. Three lipid compositions were considered: 0%, 20%, and 45% MGDG (by mole) denoted as MG-0, MG-20, and MG-45, respectively. The article is focused on the calculation of NMR dipolar interactions, which were confronted with previously reported experimental couplings. Dynamical processes and orientational distributions relevant for the averaging of dipolar interactions were evaluated. Furthermore, several parameters important for characterization of the bilayer structure, molecular organization, and dynamics were investigated. In general, only a minor change in DMPC properties was observed upon the increased MGDG/DMPC ratio, whereas properties related to MGDG undergo a more pronounced change. This effect was ascribed to the fact that DMPC is a bilayer (L(α)) forming lipid, whereas MGDG prefers a reverse hexagonal (H(II)) arrangement.

Localisation of BODIPY-labelled phosphatidylcholines in lipid bilayers

A series of sn-2 acyl-labelled phosphatidyl-cholines (PC), bearing 4,4-difluoro-1-3-5-7-tetra-methyl-4-bora-3a,4a-diaza-s-indacene-8-yl (Me(4)-BODIPY) at the end of the C(n)-acyl chains were solubilised in unilamellar vesicles and studied with respect to the order and location of the Me(4)-BODIPY (denoted: B) group. The obtained results are based on time-resolved electronic energy transfer from donors (2-(9-anthroyloxy)-stearic acid) localised in the lipid-water interface to acceptors BnPC (n = 3, 5, 7, 9, 11, 13, 15), as well as the energy migration among the Me(4)-BODIPY groups of BnPC:s. The donor-acceptor and the donor-donor experiments strongly suggest that the Me(4)-BODIPY group in BnPC tends to loop back close to the lipid-water interface. The Me(4)-BODIPY groups, residing in the two bilayer leaflets, are located at approximately the same depth, and transversally separated by ca. 27 A for all n-values. Close to the interface, the optimal transversal distribution widens somewhat with increasing length of the sn-2 acyl chain. The obtained order parameter profile of the BnPC:s is also compatible with such a location.

Power law relaxation and glassy dynamics in Lebwohl-Lasher model near the isotropic-nematic phase transition

Orientational dynamics in a liquid crystalline system near the isotropic-nematic (IN) phase transition is studied using molecular dynamics simulations of the well-known Lebwohl-Lasher model. As the IN transition temperature is approached from the isotropic side, we find that the decay of the orientational time correlation functions (OTCF) slows down noticeably, giving rise to a power law decay at intermediate time scales. The angular velocity time correlation function also exhibits a rather pronounced power law decay near the IN boundary. In the mean squared angular displacement at comparable time scales, we observe the emergence of a subdiffusive regime which is followed by a superdiffusive regime before the onset of the long-time diffusive behavior. We observe signature of dynamical heterogeneity through pronounced non-Gaussian behavior in orientational motion particularly at lower temperatures. This behavior closely resembles what is usually observed in supercooled liquids. We obtain the free energy as a function of orientational order parameter by the use of the transition matrix Monte Carlo method. The free energy surface is flat for the system considered here and the barrier between isotropic and nematic phases is vanishingly small for this weakly first-order phase transition, hence allowing large scale, collective, and correlated orientational density fluctuations. This might be responsible for the observed power law decay of the OTCFs.

Molecular dynamics simulation of the nematic liquid crystal phase in the presence of an intense magnetic field

The influence of an intense external field on the dynamics of the nematic liquid crystal phase is investigated using a molecular dynamics simulation for the Gay-Berne nematogen under isobaric-isothermal conditions. The molecular dynamics as a function of the second-rank orientational order parameter P<2> for a system consisting of a nematic liquid crystal in the presence of an intense magnetic field is compared with that of a similar system without the field. The translational motion of molecules is determined as a function of the translational diffusion coefficient tensor and the anisotropy and compared with the values predicted theoretically. The rotational dynamics of molecules is analyzed using the first- and the second-rank orientational time correlation functions. The translational diffusion coefficient parallel with respect to the director is constrained by the intense field, although the perpendicular one is decreased as the P<2> is increased, just as it is in the system without the field. However, no essential effect of the strong magnetic field is observed in the rotational molecular dynamics. Further, the rotational diffusion coefficient parallel with respect to the director obtained from the first-rank orientational time correlation function in the simulation is qualitatively in agreement with that in the real nematic liquid crystalline molecules. The P<2> dependence of the rotational diffusion coefficient for the system with the intense magnetic field shows a tendency similar to that for the system without the field.

Orientational Dynamics in the Isotropic Phase of a Calamitic Liquid-Crystal Model

We report a molecular dynamics simulation study on the isotropic phase of an idealized calamitic liquid crystal model with a length-to-width ratio of approximately 5-6. The study focuses on the characterization of single-particle and collective orientational dynamics on approaching the phase transition to the nematic phase. Recent experimental and simulation works have suggested that a power law behavior exists at relatively short times in the decay of the time derivative of the orientational correlation functions. Qualitatively, our simulation data are consistent with these findings. Both single-particle and collective time correlation function derivatives possess, in their respective log-log plots, a linear region at very short times, whose slope is essentially independent from the thermodynamic state. Nevertheless, the single-particle orientational correlation functions are better described by a function which is the sum of a fast exponential, an intermediate stretched-exponential and a slow exponential, while the collective orientational correlation functions are satisfactorily described by a sum of two exponentials, at higher density, or by just one exponential, at lower density.

A dissipative particle dynamics description of liquid-crystalline phases. I. Methodology and applications

Simulations of nematic and smectic mesophases based on a dissipative particle dynamics approach are discussed. Mesogenic units are built in the form of standard semirigid bead-spring chains. It is shown that nematic phases can be formed for chains containing at least eight beads, provided that the conservative soft-repulsive potential between nonconnected beads is sufficiently strong. Smectic phases are observed only by modifying the repulsive interaction between the main-chain and terminal beads. The simulations indicate that the smectic-nematic and smectic-isotropic phase transitions take place through the buckling of the smectic layering in the system.

Computer Simulation study of polar liquids: static and dynamic properties

The Berne-Pechukas-Kushick potential for linear molecules, together with a central electric point dipole, has been used as the model for polar liquids in a series of molecular dynamics computer simulations. Different simulations used Ewald summation, spherical cut off and spherical cut off with reaction field correction to sum the dipole-dipole interactions, and the relative merits of these methods are discussed. Results for thermodynamic properties and the distribution function h ∆ ( r ) are presented. Results for the autocorrelation functions for dipole orientation and angular velocity are also presented, and discussed in terms of memory functions, particularly with regard to the Steele perturbation theory. The complex, frequency-dependent dielectric constant has been calculated from the memory function of the autocorrelation function of the periodic cube dipole moment, and results are presented in the form of Cole-Cole plots. The ‘dielectric friction’ approach to polar liquids is examined against the evidence of the molecular dynamics data. Attention is drawn to the behaviour of the cross correlations between dipole orientations and their importance to the problem of dielectric relaxation is emphasized.