Communication: Critical dynamics and nuclear relaxation in lipid bilayers

Membrane composition fluctuations affect deuterium nuclear magnetic relaxation in lipid bilayers. The time dependence of the fluctuations depends on lipid diffusion. Near a miscibility critical point this diffusion involves an advective hydrodynamic coupling to the aqueous phase. The corresponding diffusion coefficient depends on both the critical length and the fluctuation wavelength. We calculate the effects of these dynamics on transverse deuterium nuclear relaxation in the 0.1(o)-10(o) range above the critical temperature.     

Growth pattern and electronic properties of acetonitrile clusters: a density functional study

We report a systematic theoretical study on the growth pattern and electronic properties of acetonitrile clusters [(CH(3)CN)(n) (n = 1, 9, 12)] using density functional approach at the B3LYP6-31++G(d,p) level. Although we have considered a large number of configurations for each cluster, the stability of the lowest energy isomer was verified from the Hessian calculation. It is found that the lowest energy isomer of the dimer adopts an antiparallel configuration. For trimer and tetramer, cyclic ring structures were found to be favored over the dipole stabilized structure. In general, it is found that the intermolecular CH...N interactions play a significant role in the stabilization of the cyclic layered geometry of acetonitrile clusters. A critical comparison between trimer and tetramer clusters suggests that the three member cyclic ring is more stable than four member rings. The growth motif for larger clusters (n = 5-9, 12) follows a layered pattern consisting of three or four membered rings, which, in fact, is used as the building block. Based on the stability analysis, it is found that clusters with an even number of molecular entities are more stable than the odd clusters, except trimer and nonamer. The exceptional stability of these two clusters is attributed to the formation of trimembered cyclic rings, which have been found to form the building blocks for larger clusters.     

Raman study of vibrational relaxation of acetonitrile in solution

Line widths of isotropic Raman spectra of the ν₁ (a₁) CH or CD stretching bands of acetonitrile CH₃CN and CD₃CN were measured in a number of solvents. The vibrational dephasing theory, modified for use in binary mixtures, predicts quantitatively the solvent dependence of the Raman line widths.     

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.     

Three component model of molecular dynamics in polyethylene melts —a nuclear magnetic relaxation study

Summary A three-component model of molecular dynamics in polymer melts is described. Starting from elementary processes such as the rearrangement of local defects which is directly accessible to thermal activation, longitudinal chain diffusion (reptation) and conformational fluctuations of the surrounding tube are defined as secondary motions.The three time parameters of the components show specific dependences on the molecular weight. Experimental evidence for the model and, on the other hand, the possibility to study individual components are achieved by the aid of mixtures of protonated chains with a molecular weightM ₁ in a matrix of deuterated chains with a molecular weightM ₂. The appropriate choice ofM ₁ andM ₂ allows to shift components outside of the experimentally accessible frequency range (10⁴ to 10⁸ Hz). Experimental data for diverse polyethylene fractions are presented and described by the model. The correlation length has been calculated an the basis of the fitted parameters. The result is = 8 Å.

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Zusammenfassung Ein Dreikomponentenmodell der molekularen Dynamik in Polymerschmelzen wird beschrieben. Ausgehend von Elementarprozessen wie der Umlagerung lokaler Defekte, die unmittelbar der thermischen Aktivierung unterliegt, werden als Sekundärprozesse die longitudinale Kettendiffusion (reptation) und Konformationsfluktuationen der Umgebungsröhre definiert.Die drei Zeitparameter der Komponenten hängen spezifisch vom Molekulargewicht ab. Eine experimentelle Bestätigung sowie die Möglichkeit, einzelne Komponenten getrennt zu untersuchen, ergibt sich durch Einlagerung von protonierten Ketten des MolekulargewichtsM ₁ in eine Matrix aus deuterierten Ketten des MolekulargewichtsM ₂. Die geeignete Wahl vonM ₁ undM ₂ erlaubt es, einzelne Komponenten aus dem Meßbereich (10⁴ bis 10⁸ Hz) herauszuverlagern. Es wird über Meßdaten für verschiedene Polyäthylenfraktionen berichtet. Die Korrelationslänge wird abgeschätzt zu = 8 Å.

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With 7 figures and 1 table     

The molecular origins of nonlinear response in solute energy relaxation: the example of high-energy rotational relaxation

A key step in solution-phase chemical reactions is often the removal of excess internal energy from the product. Yet, the way one typically studies this process is to follow the relaxation of a solute that has been excited into some distribution of excited states quite different from that produced by any reaction of interest. That the effects of these different excitations can frequently be ignored is a consequence of the near universality of linear-response behavior, the idea that relaxation dynamics is determined by the solvent fluctuations (which may not be all that different for different kinds of solute excitation). Nonetheless, there are some clear examples of linear-response breakdowns seen in solute relaxation, including a recent theoretical and experimental study of rapidly rotating diatomics in liquids. In this paper we use this rotational relaxation example to carry out a theoretical exploration of the conditions that lead to linear-response failure. Some features common to all of the linear-response breakdowns studied to date, including our example, are that the initial solute preparation is far from equilibrium, that the subsequent relaxation promotes a significant rearrangement of the liquid structure, and that the nonequilibrium response is nonstationary. However, we show that none of these phenomena is enough to guarantee a nonlinear response. One also needs a sufficient separation between the solute time scale and that of the solvent geometry evolution. We illustrate these points by demonstrating precisely how our relaxation rate is tied to our liquid-structural evolution, how we can quantitatively account for the initial nonstationarity of our effective rotational friction, and how one can tune our rotational relaxation into and out of linear response.     

Solvation of transmembrane proteins by isotropic membrane mimetics: a molecular dynamics study

Mixtures of organic solvents are often used as membrane mimetics in structure determination of transmembrane proteins by solution NMR; however, the mechanism through which these isotropic solvents mimic the anisotropic environment of cell membranes is not known. Here, we use molecular dynamics simulations to study the solvation thermodynamics of the c-subunit of Escherichia coli F1F0 ATP synthase in membrane mimetic mixtures of methanol, chloroform, and water with varying fractions of components as well as in lipid bilayers. We show that the protein induces a local phase separation of the solvent components into hydrophobic and hydrophilic layers, which provides the anisotropic solvation environment to stabilize the amphiphilic peptide. The extent of this effect varies with solvent composition and is most pronounced in the ternary methanol-chloroform-water mixtures. Analysis of the solvent structure, including the local mole fraction, density profiles, and pair distribution functions, reveals considerable variation among solvent mixtures in the solvation environment surrounding the hydrophobic transmembrane region of the protein. Hydrogen bond analysis indicates that this is primarily driven by the hydrogen-bonding propensity of the essential Asp(61) residue. The impact of the latter on the conformational stability of the solvated protein is discussed. Comparison with the simulations in explicit all-atom models of lipid bilayer indicates a higher flexibility and reduced structural integrity of the membrane mimetic solvated c-subunit. This was particularly true for the deprotonated form of the protein and found to be linked to solvent stabilization of the charged Asp(61).     

Solvation of the Whelk-O1 chiral stationary phase: a molecular dynamics study

Density functional theory calculations and molecular dynamics simulations are employed to explore the solvation of the Whelk-O1 chiral stationary phase. First, a semi-flexible representation of the Whelk-O1 selective molecule is extracted from an extensive series of B3LYP/6-311+ G(2d,p) calculations. The resulting model is used to build a chiral surface, including end-caps, for molecular dynamics study of the interface between solvent and Whelk-O1. Three solvent environments in common use for Whelk-O1 HPLC have been examined: a normal-phase solvent of n-hexane/2-propanol; a reversed-phase solvent of water/methanol; and a supercritical solvent of CO(2) and methanol. In each case, we analyze the interface with an emphasis on solvent composition and solvent hydrogen bonding to the Whelk-O1 selector.     

Paramagnetic nuclear relaxation study of the structure and dynamics of lyotropic lamellar phases

Lamellar phases of double tailed sodium alkyl-phosphates/water systems have been investigated by ³¹P and ¹³C relaxations enhanced by paramagnetic divalent ions exchanging rapidly among the polar heads of the surfactant molecules. In order to extract both structural and dynamic information from these experiments, the paramagnetic probes have been chosen such that their electron spin-lattice relaxation times are significantly larger (Mn²⁺, VO²⁺) or smaller (Ni²⁺) than the time scales of molecular motions generally found in the 0.1-2.0 ns range. The paramagnetic relaxation of surfactant nuclei results from intra- and intermolecular contributions, the latter corresponding to dipolar interactions in a two dimensional lattice. The sum of these contributions has been computed as an average over all accessible conformers resulting from the trans-gauche isomerizations of alkyl chains and fitted to the experimental relaxation rates at several magnetic field strengths. This procedure allows the determination of the populations of the main conformers, of the reorientational correlation times and of the lateral diffusion coefficient of the surfactant, which are sometimes difficult to obtain by other N.M.R. methods.     

Paramagnetic nuclear relaxation study of the structure and dynamics of lyotropic lamellar phases

Abstract

Lamellar phases of double tailed sodium alkyl-phosphates/water systems have been investigated by ³¹ P and ¹³ C relaxations enhanced by paramagnetic divalent ions exchanging rapidly among the polar heads of the surfactant molecules. In order to extract both structural and dynamic information from these experiments, the paramagnetic probes have been chosen such that their electron spin-lattice relaxation times are significantly larger (Mn²⁺, VO²⁺) or smaller (Ni²⁺) than the time scales of molecular motions generally found in the 0.1-2.0 ns range. The paramagnetic relaxation of surfactant nuclei results from intra- and intermolecular contributions, the latter corresponding to dipolar interactions in a two dimensional lattice. The sum of these contributions has been computed as an average over all accessible conformers resulting from the trans-gauche isomerizations of alkyl chains and fitted to the experimental relaxation rates at several magnetic field strengths. This procedure allows the determination of the populations of the main conformers, of the reorientational correlation times and of the lateral diffusion coefficient of the surfactant, which are sometimes difficult to obtain by other N.M.R. methods.     

Solvation of Co(III)-cysteinato complexes in water: a DFT-based molecular dynamics study

Structural, dynamical, and vibrational properties of complexes made of metal cobalt(III) coordinated to different amounts of cysteine molecules were investigated with DFT-based Car-Parrinello molecular dynamics (CPMD) simulations in liquid water solution. The systems are composed of Co(III):3Cys and Co(III):2Cys immersed in liquid water which are modeled by about 110 explicit water molecules, thus one of the biggest molecular systems studied with ab initio molecular simulations so far. In such a way, we were able to investigate structural and dynamical properties of a model of a typical metal binding site used by several proteins. Cobalt, mainly a toxicological agent, can replace the natural binding metal and thus modify the biochemical activity. The structure of the surrounding solvent around the metal-ligands complexes is reported in detail, as well as the metal-ligands coordination bonds, using radial distribution functions and electronic analyses with Mayer bond orders. Structures of the Cocysteine complexes are found in very good agreement with EXAFS experimental data, stressing the importance of considering the surrounding solvent in the modeling. A vibrational analysis is also conducted and compared to experiment, which strengthens the reliability of the solvent interactions with the Cocysteine complexes from our molecular dynamics simulations, as well as the dynamics of the systems. From this preliminary analysis, we could suggest a vibrational fingerprint able to distinguish Co(III):2Cys from Co(III):3Cys. Our simulations also show the importance of considering a quantum explicit solvent, as solute-to-solvent proton transfer events have been observed.     

Solvation of phenylglycine- and leucine-derived chiral stationary phases: molecular dynamics simulation study

A theoretical study of the solvation of ( R)- N-(3,5-dinitrobenzoyl)phenylglycine- and ( R)- N-(3,5-dinitrobenzoyl)leucine-derived chiral stationary phases (CSPs) is presented. Semiflexible models of the chiral selectors are prepared from B3LYP/6-311G** calculations, and these are used in the molecular dynamics simulations of the corresponding interface. The chiral interface is examined for four solvents: 100% hexane, 90:10 hexane:2-propanol, 80:20 hexane:2-propanol, and 100% 2-propanol. Despite the similarities between phenylglycine and leucine, the interfaces are distinct both in terms of the selector orientations at the surface and in the number of hydrogen bonds formed with 2-propanol. We also find that an increase in alcohol concentration alters the preferred orientations of the selectors.     

Solvation dynamics under a microscope: single giant lipid vesicle

Picosecond spectroscopy under a confocal microscope is employed to study solvation dynamics of coumarin 153 (C153) inside a single giant lipid vesicle (1,2-dilauroyl-sn-glycero-3-phosphocholine, DLPC) of diameter 20 μm. Fluorescence correlation spectroscopy (FCS) indicates that the diffusion coefficient (D(t)) of the probe (coumarin153, C153) in the immobilized vesicle displays a wide distribution from ~3 to 21 μm(2) s(-1). The distribution of D(t) suggests that the microenvironment of the probe (C153) is highly heterogeneous and the local friction is different for probe molecules in different regions. The values of D(t) is significantly smaller than that for the same dye in bulk water (550 μm(2) s(-1)). This suggests that the probe is located in the interface or membrane region rather than in the water pool of the vesicle. The solvation time of C153 in different regions of the lipid vesicle varies between 750 to 1200 ps. This result clearly shows that a confocal microscope is able to resolve the spatial heterogeneity in local friction (i.e., D(t)) and solvation dynamics within a lipid vesicle.     

Solvation of perfluorooctane and octane in water, methanol, acetonitrile, and aqueous mixtures of methanol and acetonitrile

Molecular dynamics simulations are used to examine the local solvation structure of single octane and perfluorooctane molecules in liquid water, methanol, acetonitrile, and aqueous mixtures of methanol and acetonitrile. The motivation is to obtain baseline information about the solvation of perfluorooctane by liquids used as the mobile phase in liquid chromatography and how it differs from the solvation of octane. While octane is uniformly solvated by both water and the second component, perfluorooctane is solvated by methanol and acetonitrile with the exclusion of water from the first solvation layer when the solvent is a mixture.     

Solvation dynamics and electric field relaxation in an imidazolium-PF6 ionic liquid: from room temperature to the glass transition

Time-resolved phosphorescence spectra and anisotropy of quinoxaline were measured in an ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate (BMIM-HFP), in its supercooled state near the glass-transition temperature. The solvation dynamics results are compared with the rotational motion of the probe and with the dielectric behavior of the neat ionic liquid. The dynamics in the viscous state are highly dispersive and show a super-Arrhenius temperature dependence, as typical for glass-forming materials. Combined with room-temperature results, solvation dynamics is observed to follow the structural relaxation times in terms of eta/T for more than 10 decades, from subnanoseconds at room temperature to seconds near the glass-transition temperature T(g). The dielectric modulus relaxation follows this trend only for temperatures T > 1.2T(g) and departs significantly from eta/T in the 1.1T(g) > T > T(g) range. This deviation is reminiscent of the enhanced translational diffusion or fractional Stokes-Einstein behavior observed in many fragile supercooled liquids. Because the electric field relaxation in BMIM-HFP includes dc conductivity, this correlation function involves translational motion and thus displays the effect of enhanced diffusivity. A microscopic model is required for rationalizing the decoupling of solvation dynamics from the longitudinal time scales and the limitation of this effect to the viscous regime with T < 1.2T(g).     

The role of the torsional potential in relaxation dynamics: a molecular dynamics study of polyethylene

The role of the torsional potential in bulk polymer chain dynamics is investigated via molecular dynamics simulation using polyethylene as a model system. A number of three-fold barrier values, both greater and less than the standard one, were invoked. The one-fold potential that determines the gauche vs trans energy difference was also varied. For each of the selected torsional potentials, the MD volumetric glass transition temperature, T_g, was located. It was found that T_g is quite sensitive to the three-fold barrier magnitude, moving from below 100 K to nearly 400 K as the barrier goes from zero to twice the standard value. However T_g was found to be quite insensitive to the gauche trans energy difference. Details of the conformational dynamics were studied for the case of a zero torsional potential. This included the rate and location of conformational transitions, the decay of the torsional angle autocorrelation function (ACF) and the cooperativity of conformational transitions, all as a function of temperature. The temperature dependence of the conformational transition rate remains Arrhenius at all temperatures. The relaxation time characterizing the torsional angle ACF decay exhibits WLF temperature behavior. The conformational transitions are randomly distributed over the bonds at high temperature, but near T_g they become spatially heterogeneous and localized. The transitions show next-neighbor correlation as well as self-correlated forward-backward transitions. All of these features are similar to those found in previous simulations under the standard torsional potential.