Molecular dynamics investigation of bent-core molecules on a water surface

Molecular dynamics simulations are carried out for bent-core molecules at water surfaces. The water surface is shown to alter the equilibrium molecular structure significantly by causing a different class of torsional states to become more favorable. The equilibrium structure is also altered by the substitution of chlorine atoms for hydrogen atoms on the central phenyl ring in that this substitution forces the bent core to remain in a single torsional state rather than be delocalized among several torsional states. The consequences of these structural changes on the chirality and packing of these molecules on water surfaces are discussed.     

Langmuir monolayers of bent-core molecules

A systematic study of five different, symmetric bent-core liquid crystals in Langmuir thin films at the air/water interface is presented. Both the end chains (siloxane vs hydrocarbon) and the core (more or less amphiphilic) are varied, to allow an exploration of different possible layer structures at the interface. The characterization includes systematic surface pressure isotherms, Brewster angle microscopy, and surface potential measurements. The properties of these layers are strongly dependent on the individual type of molecule: the molecules with amphiphilic end chains lie quite flat on the surface, while the molecules with hydrophobic end chains construct multilayer structures. In both cases, the three-dimensional collapse structure is reversible.     

Molecular dynamics simulations of amphiphilic graft copolymer molecules at a water/air interface

Fully atomistic molecular dynamics simulations of amphiphilic graft copolymer molecules have been performed at a range of surface concentrations at a water/air interface. These simulations are compared to experimental results from a corresponding system over a similar range of surface concentrations. Neutron reflectivity data calculated from the simulation trajectories agrees well with experimentally acquired profiles. In particular, excellent agreement in neutron reflectivity is found for lower surface concentration simulations. A simulation of a poly(ethylene oxide) (PEO) chain in aqueous solution has also been performed. This simulation allows the conformational behavior of the free PEO chain and those tethered to the interface in the previous simulations to be compared.     

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.     

Molecular dynamics simulations of liquid crystal molecules on a polyimide monolayer

Preliminary results are presented on the molecular dynamics simulations of alignment of the liquid crystal molecule, 4-n-octyl-4'-cyanobiphenyl (8CB), on a polyimide (pyromelltic dianhydride-p-phenylene diamine) oligomer monolayer. We actually simulated a three-layer system, i.e., liquid crystal molecule/polyimide oligomer/a basal plane of graphite. First, simulations of the oligomers adsorbed on graphite were done in order to obtain reasonable adsorption structures, as the pre-stage simulation of the three-layer system. Then, by placing a liquid crystal layer on top, the three-layer system was simulated. The stable liquid crystal alignment direction on the polyimide monolayer was found roughly to be the polyimide chain direction with zero pretilt in this combination of liquid crystal and polymer materials. The calculated adsorption energy of an 8CB molecule to the polyimide monolayer was 128 kJ mol^-1 and the carbonyl group of the polyimide was the main adsorption site.     

Molecular dynamics simulation of the aggregation of colloidal particles

The spontaneous time evolution of systems containing N colloidal particles (N = 12, 24, 100) in a spherical cell of volume V at a constant volume fraction φ=0.1 was studied by a molecular dynamics method in the NVT ensemble. The starting velocities of the particles are allocated according to the Maxwell distribution at T=273 K.

Pairwise interaction of the particles was specified by molecular, electrostatic and elastic forces. The changes in the potential energy of the systems were calculated during the establishment of dynamic equilibrium. Coagulation takes place at sufficiently high values of the Hamaker constant. The value of the coefficient of Brownian diffusion, which is calculated from the half-time of coagulation, is found to be close to the known value for aqueous dispersions. The inclusion of electrostatic forces prevents coagulation.

The results obtained are in agreement with those obtained using theories of aggregate formation. Some structural characteristics of aggregates and stable systems are discussed.     

High-resolution neutron-scattering study of slow dynamics of surface water molecules in zirconium oxide

We have performed a quasielastic neutron-scattering experiment on backscattering spectrometer with sub-mueV resolution to investigate the slow dynamics of surface water in zirconium oxide using the sample studied previously with a time-of-flight neutron spectrometer [E. Mamontov, J. Chem. Phys. 121, 9087 (2004)]. The backscattering measurements in the temperature range of 240-300 K have revealed a translational dynamics slower by another order of magnitude compared to the translational dynamics of the outer hydration layer observed in the time-of-flight experiment. The relaxation function of this slow motion is described by a stretched exponential with the stretch factors between 0.8 and 0.9, indicating a distribution of the relaxation times. The temperature dependence of the average residence time is non-Arrhenius, suggesting that the translational motion studied in this work is more complex than surface jump diffusion previously observed for the molecules of the outer hydration layer. The observed slow dynamics is ascribed to the molecules of the inner hydration layer that form more hydrogen bonds compared to the molecules of the outer hydration layer. Despite being slower by two orders of magnitude, the translational motion of the molecules of the inner hydration layer may have more in common with bulk water compared to the outer hydration layer, the dynamics of which is slower than that of bulk water by just one order of magnitude.     

Molecular dynamics of oligofluorenes: a dielectric spectroscopy investigation

The molecular dynamics were investigated in a series of "defect-free" oligofluorenes up to the polymer by dielectric spectroscopy (DS). The method is very sensitive to the presence of keto "defects" that when incorporated on the backbone give rise to poor optical and electronic properties. Two dielectrically active processes were found (beta and alpha process). The latter process (alpha) displays strongly temperature dependent relaxation times and temperature- and molecular weight-dependent spectral broadening associated with intramolecular correlations. The glass temperature (Tg) obeys the Fox-Flory equation and the polymer Tg is obtained by DS at 332 K. The effective dipole moment associated with the alpha process is 0.27 +/- 0.03 D.     

Molecular dynamics simulation of water in a contact with an iron pyrite FeS2 surface

A strong adsorption of the water molecules to the pyrite surface is shown by a molecular dynamic simulation of the water-iron pyrite FeS2 interface. Water molecules closest to the pyrite surface are bound by an electrostatic interaction to the iron atoms in grooves running parallel to one of the crystal axes. The grooves are about two atoms wide and are directed along 010 for the (001) surface. The position of the water-surface potential minimum and the energy of adsorption were determined by optimization for a single water molecule at the interface. At room temperature and normal density there are altogether three distinguishable layers of water above the surface. One is associated with the groove: one with H bonding to the sulphur atoms comprising the ridges separating the grooves, and the third with the soft wall boundary between the absorbed water layers and bulk region of water. Simulations were also used to explore the effect of a temperature range significant for geophysical studies.     

Molecular dynamics simulations of spontaneous bile salt aggregation

Bile salts are surfactants in bile that facilitate digestion, adsorption and excretion of various compounds. They have planar hydrophobic and hydrophilic faces and therefore exhibit some unusual properties; including the shape and size of the micelles that they form. Molecular dynamics simulations of the spontaneous aggregation of six bile salts (cholate (CHD), glycocholate (GCH), taurocholate (TCH), glycochenodeoxycholate (GCD), glycodeoxycholate (GDX) and glycolithocholate (GLC)) were performed in an aqueous phase to gain insight into their micellar structure. The aggregates that formed spontaneously from a random distribution of molecules ranged in size from 8 to 17 molecules. The structures are highly dynamic in nature and are on average oblate, but can vary from oblate, to spherical or prolate. Intermolecular hydrogen bonding within the micelles was found to be an important factor in determining the micelle size, structure and dynamics. The molecular arrangement within the micelles maximises the hydration of the hydrophilic chains and some favourable orientations for adjacent molecules were acquired. The dynamics of the micelles were investigated using the hydrogen-bond lifetime autocorrelation function correlation time, which exhibited a relationship with the degree of hydroxylation. Comparison of the proposed model to the three literature models showed some features of the disk shaped models of Cary and Small [M.C. Cary, D.M. Small, Arch. Intern. Med. 130 (1972) 506–527] and Kawamura et al. [H. Kawamura, Y. Murata, T. Yamaguchi, H. Igimi, M. Tanaka, G. Sugihara, J.P. Kratohvil, J. Phys. Chem. 93 (1989) 3321–3326], whereas the third, inverted helix model of Giglio et al. [E. Giglio, S. Loreti, N.V. Pavel, J. Phys. Chem. 92 (1988) 2858–2862] can be discounted. The proposed model is better than the existing models, which assumed a rigid and structured molecular arrangement.     

Inhomogeneity effects on the structure and dynamics of water at the surface of a membrane: a computer simulation study

The authors report the structural and dynamical properties of water interacting with the surface of a lipid bilayer. Three regions have been identified, which show different dynamical regimes of water: a region of strong water-solute interaction, a transition region, and the bulk water region. The dynamics of the strong-interacting water is dominated by caging effects, as shown by the analysis of the self-intermediate scattering function, and by the disrupture of water's hydrogen bond network, while the smooth transition to bulk water is traced back to the roughness of the bilayer surface.     

Layer-by-layer adsorption of water molecules on the surface of a silver iodide crystal

Computer simulations at the molecular level were used to analyze the mechanism of the nucleation of water condensate from the vapor phase on the surface of a silver iodide crystal at 260 K. The initial stage of the condensation process is the sequential growth of monolayers on the substrate surface without formation of a compact microdroplet. The dependence of the equilibrium work of formation of the condensate film on its thickness exhibits oscillations. The formation of layers close to the substrate surface involves the overcoming of a Gibbs energy barrier.     

Interference effects on the photoluminescence intensity of molecules near a dielectric surface

The photoluminescent intensity of a molecule near a dielectric interface has been investigated theoretically as a function of separation between the molecule and interface. The intensity is expressed by means of functions which have been derived previously. Numerical results have been calculated for the case of a luminescent coating near a semiconductor surface; these results are compared with recent experimental data on tetracene fluorescence near Si and GaAs surfaces.     

Molecular dynamics simulation study of the structural characteristics of water molecules confined in functionalized carbon nanotubes

Molecular dynamics (MD) simulations were performed to study the structural properties of water molecules confined in functionalized carbon nanotubes (CNTs). Four CNTs, two armchair-type (6, 6), (7, 7) and two zigzag-type (10, 0), (12, 0) CNTs, representing different helicities and different diameters, were chosen and functionalized at their open ends by the hydrophilic -COOH and the hydrophobic -CH3 groups. The structural properties of water molecules inside the functionalized CNTs, including the orientation distributions of dipole moment and O-H bonds, the length of the single-file water chain, and the average number of hydrogen bonds, were analyzed during a process of simulations. MD simulation results in this work showed that the -CH3 functional groups exert little special effects on the structural properties of water molecules. It is mainly due to the relatively small size of the -CH3 group and its hydrophobic nature, which is consistent with hydrophobic CNTs. For CNTs functionalized by -COOH groups, the configurations of -COOH groups, incurvature or excurvature, determine whether water molecules can enter the CNTs. The incurvature or excurvature configurations of -COOH groups are the results of synergy effects of the CNTs' helicity and diameter and control the flow direction of water molecules in CNTs.     

Plasma sputtering of water molecules from the liquid phase by low-energy ions: Molecular dynamics simulation

The ion bombardment-assisted transfer of the components of a solution to the plasma zone in an atmospheric-pressure glow discharge with a liquid cathode plays an important role. The dynamics of the impact of a 50–500 eV ion on the surface of liquid water was studied by molecular dynamics simulation. Data on the amount of water molecules transferred by ion impact to the gas phase are presented. It was shown that the sputtering yield of water can reach 450 molecules per ion at an energy consumption of 0.75 eV for sputtering. Structural changes occurring in the liquid phase under ion bombardment were analyzed on the basis of the dynamics of degradation of hydrogen bonds.     

Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface

We report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison with our previous results for two albumin fragments.     

Depth profiling of water molecules at the liquid-liquid interface using a combined surface vibrational spectroscopy and molecular dynamics approach

The studies presented here combine experimental and computational approaches to provide new insights into how water structures and penetrates into the organic phase at two different liquid-liquid systems: the interfaces of carbon tetrachloride-water (CCl4-H2O) and 1,2-dichloroethane-water (DCE-H2O). In particular, molecular dynamics simulations are performed to generate computational spectral intensities of the CCl4-H2O and DCE-H2O interfaces that are directly comparable with experimental measurements. These simulations are then applied toward the generation of spectral profiles, responses that vary as functions of both frequency and interfacial depth. These studies emphasize the similarities and differences in the structure, orientation, and bonding of interfacial water as a function of interfacial depth for these two liquid-liquid systems and demonstrate the differing behavior of water monomers that penetrate into the organic phase.     

Stretching effects on the permeability of water molecules across a lipid bilayer

Using a coarse grained molecular dynamics model of a solvent-surfactant system, we study the effects of stretching on the permeability of water across a lipid bilayer. The density profile, free energy profile, diffusion profile, and tail ordering parameter were computed for a set of stretched membranes maintained at constant area. We computed the water permeability across each membrane using the inhomogeneous solubility-diffusion model first proposed by Marrink and Berendsen [J. Phys. Chem. 98, 4155 (1994)]. We find that even though the resistance to permeation profile shows a great deal of qualitative change as the membranes are stretched, the overall permeability remains nearly constant within the relevant range of stretching. This is explained by the fact that the main barrier to permeation, located in the densest section of the tails, is insensitive to increased area per lipid, as a result of competing effects. Expansion leads to thinning and a higher density in the tail region, the latter leading to an increase in the free energy barrier. However, this is compensated by the reduction in the transverse distance to cross and a larger diffusion coefficient due to increased disordering in the chains.     

Molecular dynamics of polystyrene model molecules: Solvent effects on intramolecular excimer formation in 2,4-diphenylpentanes

Intramolecular excimer formation in 2,4-diphenylpentanes has been examined in a homologous series of alkanes, in ethanol and in mixtures of ethanol, ethylene glycol and glycerol. The ratio of the emission intensities of dimer and monomer (I_D/I_M) is not affected in low viscosity solvents but, above 4 cP, viscosity effects are discernible and a relationship of the form I_D/I_M = Aη^?2 is obeyed. In methylene chloride, only the dl molecule exhibits a decrease of the efficiency of excimer sampling. The temperature dependence of I_D/I_M in isooctane and methylene chloride has been interpreted in terms of the activation energy of the excimer sampling.