Maureen P. Neal

Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules

Molecular dynamics integrators are presented for translational and rotational motion of rigid molecules in microcanonical, canonical, and isothermal-isobaric ensembles. The integrators are all time reversible and are also, in some approaches, symplectic for the microcanonical ensembles. They are developed utilizing the quaternion representation on the basis of the Trotter factorization scheme using a Hamiltonian formalism. The structure is similar to that of the velocity Verlet algorithm. Comparison is made with standard integrators in terms of stability and it is found that a larger time step is stable with the new integrators. The canonical and isothermal-isobaric molecular dynamics simulations are defined by using a chain thermostat approach according to generalized Nosé-Hoover and Andersen methods.

Helical twisting power and scaled chiral indices

Chirality of optically active liquid crystal molecules has become an important research topic and the subject of a number of theoretical and experimental studies. We present here the results of the application of a newly developed scaling method of a chiral index to a range of chiral molecules. Good agreement is found between the scaled chiral index and the helical twisting power for relatively rigid molecules. Two flexible TADDOL (α,α,α′,α′-tetraaryl-1,3-dioxolan-4,5dimethanol) molecules are studied to determine which conformations may give rise to their high experimental helical twisting powers. A variety of links between the moment of inertia tensor, the dihedral angles, the scaled chiral indices, the minimum energy of the optimized geometry and the experimental helical twisting power are discussed. The scaled chiral and steric indices and dihedral angles are promising as predictors of experimental helical twisting power, in particular for relatively rigid molecules, in cases where all the relevant int...

A generalized scaling of a chiral index for molecules

We propose a scaling of an intrinsic molecular chirality index calculated from atomic positions. Its application to the design of chiral molecules through a consideration of atomic or group chiral indices is discussed for a range of molecules from small molecules to liquid crystal molecules. It is found to indicate the trend in change of chirality of a molecule caused by an atom or group substitution. Comparison is made between the method of scaling and an analytic calculation of the index for an orthogonal tetrahedron. We investigate the effect of substitution of atoms and groups in real liquid crystal molecules by application of the generalized chiral index.

Helical twisting power and chirality indices

We review the statistical theory of helical twisting power and propose an alternative derivation of the results obtained by Nordio and co-workers [1999, J. chem. Soc. Perkin Trans., 2, 411]. We examine chiral indices which include an interaction between the host and dopant, then compare these with chiral indices dependent only on the dopant structure. We discuss the need for the inclusion of the interaction between dopant and host in the description of chiral induction, and discuss alternative measures of chirality and their shortcomings. We show that both the previously suggested surface indices and the newly proposed one vanish for at least one class of non-trivial chiral structures. We compare the results obtained from these surface indices with a more general 3D chiral index and evaluate these indices for four helicene (M)-1–4 molecules.

Correlation between molecular chirality and helical twisting power: a computer simulation study

The helical structure of the chiral nematic phases induced by chiral dopants in nematic solvents provides a macroscopic information of the molecular chirality of the dopant. Chiral dopant molecules considered in this paper are challenging systems because their twisting ability has a relatively strong dependence on the molecular structure. Several classes of the flexible chiral dopants such as the binaphthyl derivatives characterized by a conformational chirality are investigated. In addition, we will investigate the odd–even effect on the helical twisting power of two azobenzene derivatives and the twist inversion with temperature and solvent of the (1S)-1-naphthalen-1-ylethyl amide and trans-4,5-diaryl-1,3-dioxolanes derivatives, respectively. In this work two different theoretical approaches, the surface model and the scaled chiral index, are studied which are combined with molecular dynamics simulations of the single molecule in the gas phase. The results are compared with the experimental values of the helical twisting power.

A molecular dynamics study of a steric multipole model of liquid crystal molecular geometry

We report results from a series of molecular dynamics simulations designed to study the phase behaviour of model rod-like liquid crystal molecules with different geometries interacting via the Gay-Berne potential. Following the classification of molecular geometry in terms of a multipole expansion in steric asymmetry, two models have been studied in detail: a zigzag model defined as a steric quadrupole and a triangle model defined as a longitudinal steric dipole, and comparison has been made with a cylindrical model. Results from the NVE ensemble indicate that the model steric quadrupole delays the temperature of onset of the nematic phase. Extensive simulations in the NPT ensemble demonstrate a similar trend in the temperature of onset of the smectic B phase, with a lower temperature of onset observed with the steric quadrupole than the steric dipole. Local antiparallel steric ordering within a layer was observed with the model steric dipole in the crystal B phase but not with the model steric quadrupole...

Scaled Chiral Indices for Ferroelectric Liquid Crystals

Chirality of optically active liquid crystal molecules has become an important research topic and the subject of a number of theoretical and experimental studies. We present here the results of the application of a newly developed scaling method of a steric chiral index to chiral dopant molecules and to ferroelectric molecules. Good agreement is found between the scaled chiral index and the helical twisting power for a range of rigid chiral dopant molecules. Less good agreement is found in the case of rod-like flexible ferroelectric molecular structures and polarisation.

A molecular dynamics study of a bi-disperse liquid crystal mixture using a generalized Gay–Berne potential

We report results from a constant NVE molecular dynamics simulation of a 50:50 mixture of Gay-Berne rods with axial ratios of 35 to 1 and 3 to 1. The simulation makes use of a recently developed extension of the Gay-Berne potential which allows simulation of non-equivalent anisotropic molecules with attractive interactions. There is clear evidence of pre-smectic ordering in the nematic phase. The system undergoes a well defined transition from the nematic phase to a randomly mixed smectic phase. There is some local compositional ordering within the smectic layers but no evidence of demixing. In both the nematic and smectic phases it is found that the longer molecules have a higher [S] order parameter than the shorter molecules. This difference in order parameter is at its greatest a little below the isotropic-nematic transition temperature and decreases as the smectic phase is approached.

Molecular Structure and Helical Twisting Power

The helical structure of the chiral nematic phases induced by chiral dopants in nematic solvents provides macroscopic information about the molecular chirality of the dopant. The surface model, which combines the order parameters of the dopant in nematic host phase and chirality parameters of the dopant, is a simple method to characterise the molecular properties and the induced chiral nematic phases. In this model, the representation of the molecular surface accesible from the nematic solvent plays an important role. The rolling sphere method, in common use for calculation of the molecular surface, rolls over a set of the van der Waals spheres representing constituent atoms of the molecule. In this paper we will present the effect of changing the radius of the rolling sphere on the values of the surface chirality indices. Here chiral binaphthyl molecules have been choosen since their twisting ability has a relatively strong dependence on the molecular structure. We also discuss a range of chirality indices and their dependence on the ordering strength of the solvent.

Computer simulation of bi-disperse liquid crystals: The effect of concentration on phase behaviour and structural properties

We present results from constant-NPT molecular dynamics simulations of bi-disperse liquid crystal mixtures at a range of concentrations. These simulations are performed using the generalised Gay-Berne interaction potential. We observe that the transition temperature between ordered and disordered phases varies linearly with mole fraction. Also, the layer spacing in the smectic-B phase varies approximately linearly with mole fraction. We find that the region of nematic phase stability is very narrow in the NPT ensemble, but establish it for a single-component system. The difficulty in determining this region is related to the sensitivity of the nematic phase to density fluctuations.