Cylindrical Distribution Functions Research Articles

Molecular Dynamics Simulation for the Structure of the Water Chain in a Transmembrane Peptide Nanotube

The structure of the water chain in the 8 x cyclo-(WL)(4) peptide nanotube embedded in the POPE lipid bilayer is studied by molecular dynamics simulations. The distribution profiles of water molecules along the nanotube axis proposes a wavelike pattern of the water chain in the nanotube, arraying in the form of a 1-2-1-2 file, in contrast to the single file in other nanochannels studied widely. Cylindrical distribution functions of water at different zones and potential of mean force of a water molecule along the axis suggest that the primary reason for forming the water-chain pattern is steric constraints. A novel hydrogen bond network in the nanotube is present such that each water in the alpha-plane zones forms two hydrogen bonds (as a donor) with the two water molecules in the adjacent midplane zone, and each water molecule in the midplane zones forms one hydrogen bond with the water molecule in the adjacent alpha-plane zone and a poor hydrogen bond with the carbonyl groups in the nanotube. Strong orientations of the water dipoles near the two opening ends pointing to the opposite directions are found, and the potential energy of a water O or H atom along the axis is explored to explain the water dipole orientations' reversing in the nanotube. Defects of the hydrogen bond network exist in the central gaps of the cyclic peptide nanotube.

Liquid dimethyl sulphoxide confined by carbon nanotubes

Here, we report the molecular dynamics simulation on liquid dimethyl sulphoxide (DMSO) confined by single-walled carbon nanotubes (SWCNTs) in comparison with DMSO in the bulk phase at 298 K. The local order of DMSO, analysed in terms of radial distribution functions is similar to that in the bulk except the case with the SWCNT (8, 8) where the anomalous structure pattern is realized. Meanwhile, the translational self-diffusion coefficients of DMSO in confinements are much lower then in the bulk phase (by a factor of 2–3) and correlate with a value of the SWCNT internal diameter. Using cylindrical distribution functions of DMSO atoms we elucidate that the slowdown of self-diffusion coefficient of DMSO confined in the SWCNTs is reduced by the first layer of DMSO molecules close to the SWCNT wall.

Spatial hydration structures and dynamics of phenol in sub- and supercritical water

The hydration structures and dynamics of phenol in aqueous solution at infinite dilution are investigated using molecular-dynamics simulation technique. The simulations are performed at several temperatures along the coexistence curve of water up to the critical point, and above the critical point with density fixed at 0.3 g/cm3. The hydration structures of phenol are characterized using the radial, cylindrical, and spatial distribution functions. In particular, full spatial maps of local atomic (solvent) density around a solute molecule are presented. It is demonstrated that in addition to normal H bonds with hydroxyl group of phenol, water forms pi-type complexes with the center of the benzene ring, in which H2O molecules act as H-bond donor. At ambient conditions phenol is solvated by 38 water molecules, which make up a large hydrophobic cavity, and forms on average 2.39 H bonds (1.55 of which are due to the hydroxyl group-water interactions and 0.84 are due to the pi complex) with its hydration shell. As temperature increases, the hydration structure of phenol undergoes significant changes. The disappearance of the pi-type H bonding is observed near the critical point. Self-diffusion coefficients of water and phenol are also calculated. Dramatic increase in the diffusivity of phenol in aqueous solution is observed near the critical point of simple point-charge-extended water and is related to the changes in water structure at these conditions.

Current-voltage relationship in the auroral particle acceleration region

Abstract. The current-voltage relationship in the auroral particle acceleration region has been studied statistically by the Akebono (EXOS-D) satellite in terms of the charge carriers of the upward field-aligned current. The Akebono satellite often observed field-aligned currents which were significantly larger than the model value predicted by Knight (1973). We compared the upward field-aligned current estimated by three different methods, and found that low-energy electrons often play an important role as additional current carriers, together with the high-energy primary electrons which are expected from Knight's relation. Such additional currents have been observed especially at high and middle altitudes of the particle acceleration region. Some particular features of electron distribution functions, such as "cylindrical distribution functions" and "electron conics", have often been observed coinciding with the additional currents. They indicated time variability of the particle acceleration region. Therefore, we have concluded that the low-energy electrons within the "forbidden" region of electron phase space in the stationary model often contribute to charge carriers of the current because of the rapid time variability of the particle acceleration region. "Cylindrical distribution functions" are expected to be found below the time-varying potential difference. We statistically examined the locations of "cylindrical distribution function", and found that their altitudes are related to the location where the additional currents have been observed. This result is consistent with the idea that the low-energy electrons can also carry significant current when the acceleration region changes in time.

A Two-Ellipsoid Model Based Upon A Gaussian Overlap Potential

The two-ellipsoid model (TEM) is proposed as a versatile single-site model which can be used in the study of liquid crystal phases. This TEM uses two ellipsoids to describe a molecule, one ellipsoid for the geometry and the other for the interaction strengths of the molecule. The present TEM can mimic asymmetric interactions of a liquid crystal molecule by separating the center of the interaction ellipsoid from that of the geometry ellipsoid. The potential energy surfaces of the present TEMs compare favorably with those of the corresponding Gay-Berne and the site–site models. Monte Carlo simulations with 320 particles are performed for a symmetric interaction TEM and an asymmetric interaction TEM. The asymmetric interaction TEM displays a slightly higher transition temperature than the symmetric interaction TEM indicating that asymmetric interactions can be a driving force in a phase transition. Radial and cylindrical distribution functions of two models in the isotropic phase are similar, but those in the nematic phase are quite different.

Structural study of oriented non-crystalline PET by CDF method

The two-dimensional wide angle X-ray scattering (WAXS) intensities of oriented non-crystalline polyethylene terephthalate (PET) films extended uniaxially are collected by the symmetrical transmission method; besides, the overlapped non-crystalline peaks at WAXS intensity curves, IC(K, ϕ) obtained at different azimuthal angles are also separated by computer, resulting in two peaks caused by interchain atomic scattering in the reciprocal space,KA (K = 0.122),KB (K = 0.171), and the other two peaks from intrachain atomic scattering.Kc(K = 0.310) and KD (K = 0.548); their cylindrical distribution functions (CDF). CDF(R,a) in the real space are further calcu-lated from the intensity functions, IE(K, ϕ), using sampled transforms, thereof arising in turn the peaks in the real space as,RA(R = 0.658),RB(R =0.456),Rc(R = 0.253) andRD(R = 0. 152). corresponding to KA, KB,Kc andKD. The equivalent relationships and distribution characteristics of the above-mentioned corresponding peaks in the reciprocal and real space, as well as their sources of structure are analysed theoretically and the fine structural information from oriented non-crystalline PET is in detail investigated as well.

Local structure in anisotropic systems determined by molecular dynamics simulation

In the present communication we describe the investigation of local structure using a new visualization technique. The approach is based on two-dimensional pair correlation functions derived from a molecular dynamics computer simulation. We have used this method to analyse a trajectory produced in a simulation of a nematic liquid crystal of 4-n-pentyl-4′-cyanobiphenyl (5CB) (Komolkin et al., 1994, J. chem. Phys., 101, 4103). The molecule is assumed to have cylindrical symmetry, and the liquid crystalline phase is treated as uniaxial. The pair correlation functions or cylindrical distribution functions (CDFs) are calculated in the molecular (m) and laboratory (l) frames, g m 2(z 1 2, d 1 2) and g 1 2(Z 1 2, D 1 2). Anisotropic molecular organization in the liquid crystal is reflected in laboratory frame CDFs. The molecular excluded volume is determined and the effect of the fast motion in the alkyl chain is observed. The intramolecular distributions are included in the CDFs and indicate the size of the mot...

X-ray Diffraction by Liquid-Crystalline Polymers

Abstract Following a brief introduction to how acicular molecules form liquid-crystalline (LC) arrays in polymers, relevant elements of x-ray diffraction theory are discussed. It is shown that meaningful structural information can be obtained only when molecular arrays aligned by external forces are examined, a condition that is frequently easier to achieve in polymer than in monomer arrays. The published results of x-ray studies are reviewed critically and the interpretations of recorded intensity distributions are discussed in terms of model calculations and cylindrical distribution functions. Examples cited include side-group and main-chain LC homopolymers and main-chain copolymers.

Application of cylindrical distribution functions to wide-angle X-ray scattering from oriented polymers

A systematic approach is presented for obtaining cylindrical distribution functions (CDF's) of noncrystalline polymers which have been oriented by extension. The scattering patterns and CDF's are also sharpened by the method proposed by Deas and by Ruland. Data from atactic poly(methyl methacrylate) and polystyrene are analysed by these techniques. The methods could also be usefully applied to liquid crystals.

Analysis of wide-angle X-ray diffraction patterns of aligned glassy polymers with particular references to polystyrene

Improvement of WAXD patterns from aligned glassy polymers by a numerical desmearing technique is reported. This gives a fibre type diffraction pattern that can be more easily interpreted than radial or cylindrical distribution functions. Application to atactic and quenched isotactic polystyrene shows that the molecular conformations that are found are in agreement with those deduced from i.r. and n.m.r. spectroscopy. For isotactic polystyrene there is significant agreement between the fibre pattern of the aligned glassy polymer and that of the drawn crystalline polymer.

Some comments on cylindrical distribution functions, with special reference to X-ray studies of liquid crystals

A fundamental problem of cylindrical distribution functions is that they deal with the numbers of units in cylindrical shells. The height of these shells is undefined. Consequently, the numbers of units in these shells are also undefined.

Structure of Oriented Sodium Metaphosphate Glass Fibers

The structure of oriented sodium metaphosphate glass fibers has been investigated employing cylindrical distribution functions obtained from the x-ray scattering pattern. Although this method has rarely been used, it is the only sound one available. The difficulties in interpreting the functions were eased somewhat by the use of difference, rather than complete, cylindrical distribution functions. The former are usually less cluttered with spurious peaks than are the latter. The results indicate that the NaPO3 fibers are made up of long chains of PO4 tetrahedra, and that the axes of these chains have a strong preference for lying along the fiber axis direction. Both the general appearance of the distribution functions and the results of normal distribution function calculations agree with the existence of a very high degree of orientation in the fibers. The locations of sharp peaks on the functions suggest that the individual PO4 tetrahedra have shapes similar to that found in crystalline RbPO3. In the latter material the average in-chain P–O distance is 1.62 Å and the average out-of-chain distance is 1.46 Å. Best agreement with the experimental distribution functions is obtained with a puckered version of a planar chain, in which each tetrahedron is tilted relative to the chain axis through two mutually perpendicular angles of 20° to 30° and the intratetrahedral angles are near 110°. The high effective radial resolution obtained in the difference cylindrical distribution functions, as a result of the angular resolution, suggests that the simplified cylindrical distribution function will be a useful way to study the structures of orientated amorphous polymer fibers.