Shear ordering in thin films of spherical block copolymer

We have investigated shear-induced alignment of a bilayer of spherical diblock copolymer micelles within thin films using molecular dynamics simulations at two different levels of coarse-graining. At the microscopic level, the copolymers are modeled as bead and spring chains with specific interaction potentials which produce strongly segregated spherical micelles. The simulations qualitatively reveal that long-range shear-induced ordering of hexagonally arranged micelles arises because of the tendency of micelles to pursue trajectories of minimum frictional resistance against micelles in the opposing layer. This influences their alignment in the direction of shear without them breaking apart and reforming within the time scale of the simulations. As observed in experiments, the ordering is shown to be very sensitive to the film thickness and shearing rates. To access larger lengths and longer time scales, we further coarse-grain our system to a mesoscopic level where an individual micelle is represented by a spherical particle, which interacts with other micelles through an effective potential obtained from the microscopic simulations. This approach enables us to follow the time evolution of global order from locally ordered domains. An exponentially fast growth of the orientational correlation length of the hexagonal pattern at early times, followed by a crossover to linear growth, is found in the presence of shear, in contrast to the much slower power-law scalings observed in experiments without shear.     

A new fractional wavelet approach for the simultaneous determination of ampicillin sodium and sulbactam sodium in a binary mixture

A new application of the fractional wavelet transform (FWT) was proposed for the simultaneous determination of ampicillin (AP) and sulbactam (SB) in a pharmaceutical combination for injection. FWT approach is a new powerful tool for removing noise and irrelevant information from the absorption spectra. Cardinal information having higher peak amplitude, eliminated noise, sharp peaks with shrinking width of spectral range was obtained by the application of FWT procedure to the original absorption spectra. In this paper, FWT approach was subjected to the data vector of the UV-signals obtained from AP and SB in the wavelength range of 211.5-313.8 nm. Derivative transform was applied to the original absorption signal together with its FWT generalization. The calibration graphs for AP and SB were obtained by measuring the FWT and usual derivative amplitudes at zero-crossing points. The method validation was carried out by using the synthetic mixture analysis. Our proposed FWT approach was compared with the usual derivative spectrophotometry and chemometric methods (CLS, PCR and PLS) and a good agreement was reported.     

On the calculation of time correlation functions by potential scaling

We present and analyze a general method to calculate time correlation functions from molecular dynamics on scaled potentials for complex systems for which simulation is affected by broken ergodicity. Depending on the value of the scaling factor, correlations can be calculated for times that can be orders of magnitude longer than those accessible to direct simulations. We show that the exact value of the time correlation functions of the original system (i.e., with unscaled potential) can be obtained, in principle, using an action-reweighting scheme based on a stochastic path-integral formalism. Two tests (involving a bistable potential model and a dipeptide bond-vector orientational relaxation) are exemplified to showcase the strengths, as well as the limitations of the approach, and a procedure for the estimation of the time-dependent standard deviation error is outlined.     

The Flexibility of SIMPSON and SIMMOL for Numerical Simulations in Solid-and Liquid-State NMR Spectroscopy

 Addressing the need for numerical simulations in the design and interpretation of advanced solid- and liquid-state NMR experiments, we present a number of novel features for numerical simulations based on the SIMPSON and SIMMOL open source software packages. Major attention is devoted to the flexibility of these Tcl-interfaced programs for numerical simulation of NMR experiments being complicated by demands for efficient powder averaging, large spin systems, and multiple-pulse rf irradiation. These features are exemplified by fast simulation of second-order quadrupolar powder patterns using crystallite interpolation, analysis of rotary resonance triple-quantum excitation for quadrupolar nuclei, iterative fitting of MQ-MAS spectra by combination of SIMPSON and MINUIT, simulation of multiple-dimensional PISEMA-type correlation experiments for macroscopically oriented membrane proteins, simulation of Hartman-Hahn polarization transfers in liquid-state NMR, and visualization of the spin evolution under complex composite broad-band excitation pulses.     

In search of temporal power laws in the orientational relaxation near isotropic-nematic phase transition in model nematogens

Recent Kerr relaxation experiments by Gottke et al. have revealed the existence of a pronounced temporal power law decay in the orientational relaxation near the isotropic-nematic phase transition (INPT) of nematogens of rather small aspect ratio, kappa (kappa approximately 3-4). We have carried out very long (50 ns) molecular dynamics simulations of model (Gay-Berne) prolate ellipsoids with aspect ratio 3 in order to investigate the origin of this power law. The model chosen is known to undergo an isotropic to nematic phase transition for a range of density and temperature. The distance dependence of the calculated angular pair correlation function correctly shows the emergence of a long range correlation as the INPT is approached along the density axis. In the vicinity of INPT, the single particle second rank orientational time correlation function exhibits power law decay, (t(-alpha)) with exponent alpha approximately 2/3. More importantly, we find the sudden appearance of a pronounced power-law decay in the collective part of the second rank orientational time correlation function at short times when the density is very close to the transition density. The power law has an exponent close to unity, that is, the correlation function decays almost linearly with time. At long times, the decay is exponential-like, as predicted by Landau-de Gennes mean field theory. Since Kerr relaxation experiments measure the time derivative of the collective second rank orientational pair correlation function, the simulations recover the near independence of the signal on time observed in experiments. In order to capture the microscopic essence of the dynamics of pseudonematic domains inside the isotropic phase, we introduce and calculate a dynamic orientational pair correlation function (DOPCF) obtained from the coefficients in the expansion of the distinct part of orientational van Hove time correlation function in terms of spherical harmonics. The DOPCF exhibits power law relaxation when the pair separation length is below certain critical length. The orientational relaxation of a local director, defined in terms of the sum of unit vectors of all the ellipsoidal molecules, is also found to show slow power law relaxation over a long time scale. These results have been interpreted in terms of a newly developed mode coupling theory of orientational dynamics near the INPT. In the present case, the difference between the single particle and the collective orientational relaxation is huge which can be explained by the frequency dependence of the memory kernel, calculated from the mode coupling theory. The relationship of this power law with the one observed in a supercooled liquid near its glass transition temperature is explored.     

Dynamic Monte Carlo simulations of anisotropic colloids

We put forward a simple procedure for extracting dynamical information from Monte Carlo simulations, by appropriate matching of the short-time diffusion tensor with its infinite-dilution limit counterpart, which is supposed to be known. This approach - discarding hydrodynamics interactions - first allows us to improve the efficiency of previous dynamic Monte Carlo algorithms for spherical Brownian particles. In the second step, we address the case of anisotropic colloids with orientational degrees of freedom. As an illustration, we present a detailed study of the dynamics of thin platelets, with emphasis on long-time diffusion and orientational correlations.     

Slow dynamics of thin nematic films in the presence of adsorbed nanoparticles

Recent experiments indicate that liquid crystals can be used to optically report the presence of biomolecules adsorbed at solid surfaces. In this work, numerical simulations are used to investigate the effects of biological molecules, modeled as spherical particles, on the structure and dynamics of nematic ordering. In the absence of adsorbed particles, a nematic in contact with a substrate adopts a uniform orientational order, imposed by the boundary conditions at this surface. It is found that the relaxation to this uniform state is slowed down by the presence of a small number of adsorbed particles. However, beyond a critical concentration of adsorbed particles, the liquid crystal ceases to exhibit uniform orientational order at long times. At this concentration, the domain growth is characterized by a first regime where the average nematic domain size LD obeys the scaling law LDt approximately t1/2; at long times, a slow dynamics regime is attained for which LD tends to a finite value corresponding to a metastable state with a disordered texture. The results of simulations are consistent with experimental observations.     

Orientational dynamics of water confined on a nanometer length scale in reverse micelles

The time-resolved orientational anisotropies of the OD hydroxyl stretch of dilute HOD in H(2)O confined on a nanometer length scale in sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles are studied using ultrafast infrared polarization and spectrally resolved pump-probe spectroscopy, and the results are compared to the same experiments on bulk water. The orientational anisotropy data for three water nanopool sizes (4.0, 2.4, and 1.7 nm) can be fitted well with biexponential decays. The biexponential decays are analyzed using a wobbling-in-a-cone model that involves fast orientational diffusion within a cone followed by slower, full orientational relaxation. The data provide the cone angles, the diffusion constants for motion within the cones, and the final diffusion constants as a function of the nanopool size. The two processes can be interpreted as a local angular fluctuation of the OD and a global hydrogen bond network rearrangement process. The trend in the relative amplitudes of the long and short exponential decays suggest an increasing rigidity as the nanopool size decreases. The trend in the long decay constants indicates a longer hydrogen bond network rearrangement time with decreasing reverse micelle size. The anisotropy measurements for the reverse micelles studied extrapolate to approximately 0.33 rather than the ideal value of 0.4, suggesting the presence of an initial inertial component in the anisotropy decay that is too fast to resolve. The very fast decay component is consistent with initial inertial orientational motion that is seen in published molecular-dynamics simulations of water in AOT reverse micelles. The angle over which the inertial orientational motion occurs is determined. The results are in semiquantitative agreement with the molecular-dynamics simulations.     

The Flexibility of SIMPSON and SIMMOL for Numerical Simulations in Solid-and Liquid-State NMR Spectroscopy

Summary.  Addressing the need for numerical simulations in the design and interpretation of advanced solid- and liquid-state NMR experiments, we present a number of novel features for numerical simulations based on the SIMPSON and SIMMOL open source software packages. Major attention is devoted to the flexibility of these Tcl-interfaced programs for numerical simulation of NMR experiments being complicated by demands for efficient powder averaging, large spin systems, and multiple-pulse rf irradiation. These features are exemplified by fast simulation of second-order quadrupolar powder patterns using crystallite interpolation, analysis of rotary resonance triple-quantum excitation for quadrupolar nuclei, iterative fitting of MQ-MAS spectra by combination of SIMPSON and MINUIT, simulation of multiple-dimensional PISEMA-type correlation experiments for macroscopically oriented membrane proteins, simulation of Hartman-Hahn polarization transfers in liquid-state NMR, and visualization of the spin evolution under complex composite broad-band excitation pulses. Corresponding authors. E-mail: tv@chem.au.dk, ncn@imsb.au.dk Received June 27, 2002; accepted July 8, 2002     

Testing the use of molecular dynamics to simulate fluorophore motions and FRET

Fluorescence resonance energy transfer (FRET) is commonly used to determine the proximity of fluorophores, but usually many assumptions are required to gain a quantitative relationship between the likelihood of energy transfer and fluorophore separation. Molecular Dynamics (MD) simulations provide one way of checking these assumptions, but before using simulations to study complex systems it is important to make sure that they can correctly model the motions of fluorophores and the likely FRET efficiency in a simple system. Here we simulate a well characterised situation of independent fluorophores in solution so that we can compare the predictions with expected values. Our simulations reproduce the experimental fluorescence anisotropy of Alexafluor488 and predict that of AlexaFluor568. At the ensemble level we are able to reproduce the expected isotropic and dynamic motion of the fluorophores as well as the FRET efficiency of the system. At the level of single donor-acceptor pairs, however, very long simulations are required to adequately sample the translational motion of the fluorophores and more surprisingly also the rotational motion. Our studies demonstrate how MD simulations can be used in more complex systems to check if the dynamic orientation averaging regime applies, if the fluorophores have isotropic orientational motion, to calculate the likely values of the orientation factor κ(2) and to determine the FRET efficiency of the system in both dynamic and static orientational averaging regimes. We also show that it is possible in some situations to create system specific relationships between FRET efficiency and fluorophore separation that can be used to interpret experimental data and find any correlations between κ(2) and separation that may influence distance measurements.     

Testing the core/shell model of nanoconfined water in reverse micelles using linear and nonlinear IR spectroscopy

A core/shell model has often been used to describe water confined to the interior of reverse micelles. The validity of this model for water encapsulated in AOT/isooctane reverse micelles ranging in diameter from 1.7 to 28 nm (w0 = 2-60) and bulk water is investigated using four experimental observables: the hydroxyl stretch absorption spectra, vibrational population relaxation times, orientational relaxation rates, and spectral diffusion dynamics. The time dependent observables are measured with ultrafast infrared spectrally resolved pump-probe and vibrational echo spectroscopies. Major progressive changes appear in all observables as the system moves from bulk water to the smallest water nanopool, w0 = 2. The dynamics are readily distinguishable for reverse micelle sizes smaller than 7 nm in diameter (w0 = 20) compared to the response of bulk water. The results also demonstrate that the size dependent absorption spectra and population relaxation times can be quantitatively predicted using a core-shell model in which the properties of the core (interior of the nanopool) are taken to be those of bulk water and the properties of the shell (water associated with the headgroups) are taken to be those of w0 = 2. A weighted sum of the core and shell components reproduces the size dependent spectra and the nonexponential population relaxation dynamics. However, the same model does not reproduce the spectral diffusion and the orientational relaxation experiments. It is proposed that, when hydrogen bond structural rearrangement is involved (orientational relaxation and spectral diffusion), dynamical coupling between the shell and the core cause the water nanopool to display more homogeneous dynamics. Therefore, the absorption spectra and vibrational lifetime decays can discern different hydrogen bonding environments whereas orientational and spectral diffusion correlation functions predict that the dynamics are size dependent but not as strongly spatially dependent within a reverse micelle.     

Quantification of global orientational order in organic solids by magic-angle spinning deuterium NMR with rotor synchronization

A new method for the characterization of orientational order in organic solids based on magic-angle spinning NMR spectroscopy is introduced. The method is related to the rotor-synchronized magic-angle spinning experiment proposed by Harbison and Spiess [Chem. Phys. Lett. 124, 128 (1986)], but exploits the anisotropy of the deuterium quadrupolar coupling instead of the carbon-13 chemical shielding anisotropy. Magic-angle spinning provides a sensitivity advantage over pseudostatic techniques; using the deuterium quadrupolar coupling makes the method applicable to systems that do not exhibit large carbon chemical shift anisotropies, such as aliphatic polymers. Due to the magnitude of the deuterium quadrupolar coupling, a large number of spinning sidebands can be reliably observed, allowing for a precise determination of the orientational distribution function. Experimental data are analyzed in terms of Wigner matrix basis functions as well as the conjugate orthogonal functions framework. Unidirectionally cold-drawn poly(ethylene) is used as an example to demonstrate the method.     

Rotational averaging and optimization of laser-induced population transfer in molecules

The dynamics of a molecule subject to a short laser pulse is investigated, with focus on the averaging over initial rotational states and on the optimization of laser parameters for the efficient population transfer between vibrational and electronic states. A relation is established between final-state populations obtained with a fixed orientation and those based on a full treatment of the rotational degrees of freedom. In the short-pulse approximation, rotational averaging amounts to integrating the fixed molecule results over all orientations. The theory is applied to a variety of model systems and verified with numerical calculations using Gaussian pulses. We calculate target state populations with three procedures, optimizing the laser pulse for a fixed orientation without orientational averaging, averaging without changing the laser parameters, and reoptimizing the parameters after averaging. The analysis of the two-level system provides a reference for the order of magnitude of the effects of averaging. The three-level system brings out the relevant role of the geometry of polarization vectors and transition dipoles. The multiphoton excitation of a Morse oscillator shows the importance of taking into account the dependence of resonance frequencies on the laser intensity. Within a proton transfer model we discuss the results obtained with and without chirping and we show that "optimizing after averaging" can be as effective as choosing a more refined pulse shape.     

Simulated glass transition in free‐standing thin polystyrene films

In this article, we investigate the glass transition in polystyrene melts and free‐standing ultra‐thin films by means of large‐scale computer simulations. The transition temperatures are obtained from static (density) and dynamic (diffusion and orientational relaxation) measurements. As it turns out, the glass transition temperature of a 3 nm thin film is ～60 °K lower than that of the bulk. Local orientational mobility of the phenyl bonds is studied with the help of Legendre polynomials of the second‐order P₂(t). The α and β relaxation times are obtained from the spectral density of P₂(t). Our simulations reveal that interfaces affect α and β‐relaxation processes differently. The β relaxation rate is faster in the center of the film than near a free surface; for the α relaxation rate, an opposite trend is observed. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1160–1167, 2010     

Gas chromatography/mass spectrometry demonstration of steryl glycosides in eucalypt wood, Kraft pulp and process liquids.

The occurrence of steryl glycosides (SG) and acyl steryl glycosides (ASG) in eucalypt (Eucalyptus globulus) wood has been investigated. These compounds were analyzed as their trimethylsilyl ethers by gas chromatography/mass spectrometry (GC/MS) using a 15 m length high-temperature capillary column with a thin film, and identified on basis of their mass spectra and relative retention times comparing with those of authentic standards. Significant amounts of SG were identified in eucalypt wood whilst only traces of ASG could be detected. Eucalypt SG and ASG occur in the pyranoside form, which is readily distinguishable from the furanoside configuration by the mass spectra of their trimethylsilyl derivatives. The sterol part of the SG and ASG consisted of sitosterol, being sitosteryl 3beta-D-glucopyranoside and sitosteryl (6'-O-palmitoyl)-3beta-D-glucopyranoside, the major SG and ASG found in E. globulus wood. The presence of SG and ASG was also investigated after kraft cooking by analyzing unbleached pulp and process water samples. The GC/MS results also revealed the presence of sitosteryl 3beta-D-glucopyranoside in these samples. By contrast, no ASG could be detected. Therefore, we have shown that SG survive the kraft cooking and can be found at least partly intact after pulping, being a possible cause for pitch deposits together with free and esterified sterols.     

Molecular dynamics investigation of a density-driven glass transition in a liquid crystal system

Molecular dynamics simulations are carried out to address the density-driven glass transition in a system of rodlike particles that interact with the Gay-Berne potential. Since crystallization occurs in this system on the time scale of the simulations, direct simulation of the glass transition is not possible. Instead, glasses with isotropic orientational order are heated to a temperature T, and the relaxation times by which nematic orientational order develops are determined. These relaxation times appear to diverge at a critical density rho(c); i.e., the system can equilibrate at rhorho(c) (at the temperature T). The relaxation times follow a power-law scaling as the critical density is approached, suggesting that this density-driven glass transition concurs with mode coupling theory.     

Dynamics in supercooled ionic organic liquids and mode coupling theory analysis

Optically heterodyne-detected optical Kerr effect experiments are applied to study the orientational dynamics of the supercooled ionic organic liquids N-propyl-3-methylpyridinium bis(trifluoromethylsulfonyl)imide (PMPIm) and 1-ethyl-3-methylimidazolium tosylate (EMImTOS). The orientational dynamics are complex with relaxation involving several power law decays followed by a final exponential decay. A mode coupling theory (MCT) schematic model, the Sj?gren model, was able to reproduce the PMPIm data very successfully over a wide range of times from 1 ps to hundreds of ns for all temperatures studied. Over the temperature range from room temperature down to the critical temperature Tc of 231 K, the OHD-OKE signal of PMPIm is characterized by the intermediate power law t(-1.00+/-0.04) at short times, a von Schweidler power law t(-0.51+/-0.03) at intermediate times, and a highly temperature-dependent exponential (alpha relaxation) at long times. This form of the decay is identical to the form observed previously for a large number of organic van der Waals liquids. MCT analysis indicates that the theory can explain the experimental data very well for a range of temperatures above Tc, but as might be expected, there are some deviations from the theoretical modeling at temperatures close to Tc. For EMImTOS, the orientational dynamics were studied on the ps time scale in the deeply supercooled region near its glass transition temperature. The orientational relaxation of EMImTOS clearly displays the feature associated with the boson peak at approximately 2 ps, which is the first time domain evidence of the boson peak in ionic organic liquids. Overall, all the dynamical features observed earlier for organic van der Waals liquids using the same experimental technique are also observed for organic ionic liquids.     

A new quasiclassical method for modeling the high-resolution spectra of polyatomic systems

A new quasiclassical method for quantum autocorrelation functions based on the semiclassical limit in Wigner phase space has been derived. Unlike the existing quasiclassical method, the new method enables long-time simulations, thus making it possible to locate quantum spectral lines very precisely. The new method has been tested for a one-dimensional anharmonic oscillator fitted to the H(2) molecule and for a six-dimensional calculation of the Ar(2)I van der Waals cluster in adiabatic approximation. The obtained results compare well with the benchmark quantum-mechanical calculations and are also roughly comparable to the experimental Ar(2)I(-) zero-kinetic-energy photoelectron spectrum, which is available in the literature.     

Multiple short time power laws in the orientational relaxation of nematic liquid crystals

Relaxation in the nematic liquid crystalline phase is known to be sensitive to its proximity to both isotropic and smectic phases. Recent transient optical Kerr effect (OKE) studies have revealed, rather surprisingly, two temporal power laws at short to intermediate times and also an apparent absence of the expected exponential decay at longer times. In order to understand this unusual dynamics, we have carried out extensive molecular dynamics simulations of transient OKE and related orientational time correlation functions in a system of prolate ellipsoids (with aspect ratio equal to 3). The simulations find two distinct power laws, with a crossover region, in the decay of the orientational time correlation function at short to intermediate times (in the range of a few picoseconds to a few nanoseconds). In addition, the simulation results fail to recover any long time exponential decay component. The system size dependence of the exponents suggests that the first power law may originate from the local orientational density fluctuations (like in a glassy liquid). The origin of the second power law is less clear and may be related to the long range fluctuations (such as smecticlike density fluctuations)--these fluctuations are expected to involve small free energy barriers. In support of the latter, the evidence of pronounced coupling between orientational and spatial densities at intermediate wave numbers is presented. This coupling is usually small in normal isotropic liquids, but it is large in the present case. In addition to slow collective orientational relaxation, the single particle orientational relaxation is also found to exhibit slow dynamics in the nematic phase in the long time.     

Conformational free energies of 1,2-dichloroethane in nanoconfined methanol

Monte Carlo simulations have been used to construct free energy surfaces of 1,2-dichloroethane dissolved in methanol confined in hydrophobic spherical cavities of varying size (10-15 A) and solution density (0.6-0.79 g/cm3). The free energy surfaces are functions of two variables: the (center-of-mass) distance from the cavity wall of 1,2-dichloroethane and the Cl-C-C-Cl dihedral angle. Umbrella sampling and the weighted histogram analysis method were used to obtain accurate results for the free energy in these two degrees of freedom. Our results indicate that the conformational equilibrium and the barrier to internal rotation of the 1,2-dichloroethane depend on the position in the cavity. The results are discussed in the context of the solvent density, orientational distributions, and packing effects.