Cage Dynamics Research Articles

Monitoring Structural Transitions in Icosahedral Virus Protein Cages by Site-Directed Spin Labeling

This work describes an approach for calculating and measuring dipolar interactions in multispin systems to monitor conformational changes in icosahedral protein cages using site-directed spin labeling. Cowpea chlorotic mottle virus (CCMV) is used as a template that undergoes a pH-dependent reversible capsid expansion wherein the protein cage swells by 10%. The sequence-position-dependent geometric presentation of attached spin-label groups provides a strategy for targeting amino acid residues most probative of structural change. The labeled protein cage residues and structural transition were found to affect the local mobility and dipolar interactions of the spin label, respectively. Line-shape changes provided a spectral signature that could be used to follow the conformational change in CCMV coat dynamics. The results provide evidence for a concerted swelling process in which the cages exist in only two structural forms, with essentially no intermediates. This methodology can be generalized for all symmetry types of icosahedral protein architectures to monitor protein cage dynamics.

The effect of host relaxation and dynamics on guest molecule dynamics in H2/tetrahydrofuran-hydrate

We use ab initio molecular dynamics simulations to obtain classically the effects of H2O cage motions on the potential-energy surface (PES) of encapsulated H2 in the H2/tetrahydrofuran-hydrate system. The significant differences between the PES for the H2 in rigid and flexible cages that we find will influence calculation of the quantum dynamics of the H2. Part of these differences arises from the relaxation of the H2O cage around the classical H2, with a second part arising from the coupling of both translational and rotational motions of H2 with the H20 cage. We find that isotopic substitution of 2H for 1H of the H2O cage affects the coupling, which has implications for experiments that require the use of 2H2O, including inelastic neutron scattering that uses 2H2O cages in order to focus on the H2 guest dynamics. Overall, this work emphasizes the importance of taking into account cage dynamics in any approach used to understand the dynamics of H2 guests in porous framework materials.

Universal scaling between structural relaxation and caged dynamics in glass-forming systems: Free volume and time scales

It is shown that the Debye–Waller factor (DW), a measure of the cage dynamics, is contributed by free-volume in o-terphenyl (OTP) and glycerol. An elementary ansatz provides an alternative way to get the reduced DW from Positron Annihilation Lifetime Spectroscopy (PALS). The ansatz supports the scaling of the slow relaxation with the fast caged dynamics over about ten decades in relaxation times in OTP and glycerol. Both PALS and neutron scattering experiments show that, in order to evidence the scaling, the observation times must be shorter than the time scales of the relaxation processes.

Solvent-Dependent Cage Dynamics of Small Nonpolar Radicals: Lessons from the Photodissociation and Geminate Recombination of Alkylcobalamins

Time-resolved transient absorption spectroscopy was used to investigate the primary geminate recombination and cage escape of alkyl radicals in solution over a temperature range from 0 to 80 degrees C. Radical pairs were produced by photoexcitation of methyl, ethyl, propyl, hexylnitrile, and adenosylcobalamin in water, ethylene glycol, mixtures of water and ethylene glycol, and sucrose solutions. In contrast to previous studies of cage escape and geminate recombination, these experiments demonstrate that cage escape for these radical pairs occurs on time scales ranging from a hundred picoseconds to over a nanosecond as a function of solvent fluidity and radical size. Ultrafast cage escape (<100 ps) is only observed for the methyl radical where the radical pair is produced through excitation to a directly dissociative electronic state. The data are interpreted using a unimolecular model with competition between geminate recombination and cage escape. The escape rate constant, k(e), is not a simple function of the solvent fluidity (T/eta) but depends on the nature of the solvent as well. The slope of k(e) as a function of T/eta for the adenosyl radical in water is in near quantitative agreement with the slope calculated using a hydrodynamic model and the Stokes-Einstein equation for the diffusion coefficients. The solvent dependence is reproduced when diffusion constants are calculated taking into account the relative volume and mass of both solvent and solute using the expression proposed by Akgerman (Akgerman, A.; Gainer, J. L. Ind. Eng. Chem. Fundam. 1972, 11, 373-379). Rate constants for cage escape of the other radicals investigated are consistently smaller than the calculated values suggesting a systematic correction for radical size or coupled radical pair motion.

Vibrational relaxation of trapped molecules in solid matrices: OH(A Σ2+;v=1)/Ar

The vibrational relaxation of OH(A (2)Sigma(+);v=1) embedded in solid Ar has been studied over 4-80 K. The interaction model is based on OH undergoing local motions in a cage formed by a face-centered cubic stacking where the first shell atoms surround the guest and connect it to the heat bath through 12 ten-atom chains. The motions confined to the cage are the local translation and libration-rotation of OH and internal vibrations in OH...Ar, their energies being close to or a few times the energies of nearby first shell and chain atoms. The cage dynamics are studied by solving the equations of motion for the interaction between OH and first shell atoms, while energy propagation to the bulk phase through lattice chains is treated in the Langevin dynamics. Calculated energy transfer data are used in semiclassical procedure to obtain rate constants. In the early stage of interaction, OH transfers its energy to libration-rotation intramolecularily and then to the vibrations of the first shell and chain atoms on the time scale of several picoseconds. Libration-to-rotational transitions dispense the vibrational energy in small packages comparable to the lattice frequencies for ready flow. Energy propagation from the chains to the heat bath takes place on a long time scale of 10 ns or longer. Over the solid argon temperature range, the rate constant is on the order of 10(6) s(-1) and varies weakly with temperature.

Non-Gaussian effects in the cage dynamics of polymers

The correlation between the fast cage dynamics and structural relaxation is investigated in a model polymer system. It is shown that the cage vibration amplitude, as expressed by the Debye–Waller factor, and the relaxation time τα collapse on a single universal curve with a simple analytic form when the temperature, the density, the chain length and the monomer–monomer interaction potential are changed. For the physical states with the same τα the coincidence of the mean-square displacement, the intermediate scattering function and the non-Gaussian parameter is observed in a wide time window spanning from the ballistic regime to the onset of the Rouse dynamics driven by the chain connectivity. The role of the non-Gaussian effects is discussed.

Toward Calculations of the 129Xe Chemical Shift in Xe@C60 at Experimental Conditions: Relativity, Correlation, and Dynamics

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized continuum model are found to be very small.

Gauche conformation of acyclic guest molecules appearing in the large cages of structure-H clathrate hydrates

In the present study, measurements and analyses were made of the High-Power Decoupling (HPDEC) solid-state 13C NMR spectra of structure-H (sH) methane hydrates with isopentane, one of the simplest and smallest acyclic large guest molecules, and methylcyclohexane (MCH), a commonly used cyclic guest molecule that is larger than isopentane. From the spectroscopic information, clear and definite evidence for the molecular conformation of acyclic guest molecules that are sufficiently small so as to be entrapped into the structure-H large cage (sH-L) was expected. The 13C NMR chemical shift change was additionally checked through the use of a hydrogen-hydrogen steric perturbation model. From the overall results, we concluded that one of the smallest acyclic guest molecules, isopentane, participating in the formation of a structure-H clathrate hydrate is encaged, confirming the gauche conformation in large cavities. The present results strongly suggest that the guest position and structure in hydrate cages are greatly influenced by both short-range interactions between guest molecules and cage frameworks and long-range interactions between small and large guests. Accordingly, cage dynamics must be carefully considered when a specific sH hydrate is designed and synthesized for the purpose of tuning material properties.

Femtosecond Pump−Probe Transient Absorption Study of the Photolysis of [Cp‘Mo(CO)3]2 (Cp‘ = η5-C5H4CH3): Role of Translational and Rotational Diffusion in the Radical Cage Effect

Femtosecond pump-probe studies of the photodissociation and subsequent radical cage pair recombination dynamics of the organometallic dimer [Cp'Mo(CO)3]2 (Cp' = eta5-C5H4CH3) are reported. The dynamics following photodissociation were studied in numerous noncoordinating hydrocarbon solvents. The results indicate that primary geminate recombination occurs on an ultrafast time scale (tau approximately 5 ps) and the efficiency of cage escape is inversely proportional to solvent viscosity. Investigation of the time-dependent anisotropy in this system allowed for an estimate of the rotational correlation time of the radical fragments (tau approximately 5-25 ps). Comparison of the rates of rotational motion with the population kinetics shows that the primary solvent cage dynamics and recombination efficiency are controlled by radical diffusion and not by radical rotation.

Subdiffusion and Cage Effect in a Sheared Granular Material

We investigate experimentally the diffusion properties of a bidimensional bidisperse dry granular material under quasistatic cyclic shear. The comparison of these properties with results obtained both in computer simulations of hard spheres systems and Lennard-Jones liquids and experiments on colloidal systems near the glass transition demonstrates a strong analogy between the statistical behavior of granular matter and these systems, despite their intrinsic microscopic differences (thermal vs athermal). More specifically, we study in detail the cage dynamics responsible for the subdiffusion in the slow relaxation regime, and obtain the values of relevant time and length scales.

Moored Fish Cage Dynamics in Waves and Currents

Recent work in the area of open ocean aquaculture system dynamics has focused separately upon either the response of fish cages in waves or the steady drag response due to ocean currents. In reality, however, forcing on these open ocean structures is a nonlinear, multidirectional combination of both wave and current profiles. At the University of New Hampshire-operated Open Ocean Aquaculture site, data were collected from a wave measurement buoy and a downward-looking Acoustic Doppler Current Profiler to characterize the surface elevation and water velocity profiles during an extreme northeast storm event. In addition to waves and currents, fish cage motion response in heave, surge, and pitch was inferred from accelerometer measurements during the same storm. The environmental data sets obtained during the peak of the storm were processed, analyzed, and used as input to a dynamic finite-element model. Simulations were performed using three load case scenarios: 1) in both waves and currents; 2) in waves only; and 3) in currents only. Model motion response results in both the time and frequency domain were compared with data obtained in situ . In addition to the motion response tests, the wave and current forcing influencing the mooring line tension response was also investigated. Analysis shows that in this case, the currents do not severely influence the oscillatory motion response, but do cause the cage to tilt, layback, and sink. The wave and current interaction effect did, however, influence the anchor line loads with a portion being attributed to nonlinear effects.

Cage Instabilities in Cylindrical Roller Bearings

A six-degree-of-freedom model was developed and used to simulate the motion of all elements in a cylindrical roller bearing. Cage instability has been studied as a function of the roller-race and roller-cage pocket clearances for light-load and high-speed conditions. The effects of variation in inner race speed, misalignment, cage asymmetry, and varying size of one of the rollers have been investigated. In addition, three different roller profiles have been used to study their impact on cage dynamics. The results indicate that the cage exhibits stable motion for small values of roller-race and roller-cage pocket clearances. A rise in instability leads to discrete cage-race collisions with high force magnitudes. Race misalignment leads to a rise in instability for small roller-cage pocket clearances since skew control is provided by the sides of the cage pocket. One roller of larger size than the others causes inner race whirl and leads to stable cage motion for small roller-race clearances without any variation in roller-cage pocket clearance. Cage asymmetry and different roller profiles have a negligible impact on cage motion.

Shear banding phenomena in ultrasoft colloidal glasses

We explore the nonlinear rheological response of a soft gel formed by a crowded colloidal star polymer and focus on the occurrence of a stress plateau, marked hysteresis, and yield stress in its flow curve. With the aid of nuclear magnetic resonance velocimetry we find evidence for fluctuations in the flow behavior across the gap of the concentric cylindrical Couette device, in association with a degree of apparent slip at the inner wall. The time scale of the these fluctuations appears rapid (with respect to the measurement time per shear rate in the flow curve), on the order of tens to hundreds of milliseconds, with the speed of fluctuations associated with the flow history of the sample. Our velocity profile analysis suggests a qualitative model in which intermittent changes due to jamming/unjamming transitions occur, analogous to cage dynamics in colloidal glasses.

Electron spin relaxation due to small-angle motion: Theory for the canonical orientations and application to hierarchic cage dynamics in ionomers

Analytical expressions for transverse electron spin relaxation induced by small angle motion were derived for the first time within an anisotropic model for rotational diffusion by using an approximation of the spin Hamiltonian and its variation during reorientation that is valid close to the canonical orientations. The dependence of the decay of the stimulated echo on such motion was studied by extensive Monte Carlo simulations and regimes were identified in which the time constant of this decay is related to parameters of the anisotropic diffusion model by simple equations. For testing these theoretical findings and obtaining insight into hierarchical cage dynamics in soft matter, high-field electron paramagnetic resonance (EPR) measurements were performed at a frequency of 94 GHz where the canonical orientations for nitroxide spin labels are well resolved. A combination of continuous wave EPR, saturation recovery measurements, and measurements of the decay of primary and stimulated electron spin echoes was employed to cover time scales from a few picoseconds up to several microseconds. Ionic spin probes attached by electrostatic interactions to the surface of ionic clusters in ionomers were used as a model system in which slow cage reorientation can be studied in the glass transition region of the polymer (0.64&amp;lt;T/Tg&amp;lt;1.05). Three hierarchical reorientation processes of the spin probe were observed on different time scales. The spin probe undergoes fast intramolecular libration on the time scale of a few picoseconds, it experiences a local rearrangement of the cage on the time scale of hundreds of nanoseconds and it performs cooperative reorientation coupled to the structural relaxation of the glassy matrix over time scales comparable to or longer than several microseconds in the glass transition region.

Confinement effects on the slow dynamics of a supercooled polymer melt: Rouse modes and the incoherent scattering function.

Results of large-scale molecular-dynamics simulations of a supercooled polymer film are presented (F. Varnik, J. Baschnagel, K. Binder, J. Phys. IV 10, 239 (2000)). The dynamic and static properties of the system are studied for a wide range of film thicknesses (from 3 to about 55 times the bulk radius of gyration) and temperatures (from the normal liquid state to the supercooled region). The system is confined between two completely smooth and purely repulsive walls. Motivated by the previous results on the enhancement of the local relaxation dynamics due to the confinement (F. Varnik, J. Baschnagel, K. Binder, Eur. Phys. J. E 8, 175 (2002); Phys. Rev. E. 65, 021507 (2002)), we now study the effect of the walls on the dynamics of the Rouse modes. It has been reported from Monte Carlo studies of the Bond Fluctuation Model (BFM) that, contrary to the enhancement of the "cage dynamics" (exemplified by a faster relaxation of the incoherent scattering function in the film), Rouse modes exhibit a slower relaxation in the confined system (C. Mischler, J. Baschnagel, K. Binder, Adv. Colloid Interface Sci. 94, 197 (2001)). However, we do not observe such a discrepancy for our continuum model: At a given temperature, the relaxation of a given Rouse mode is faster in the film than in the bulk in accordance with the acceleration of the dynamics around the cage.

Fish cage and mooring system dynamics using physical and numerical models with field measurements

As wild fish stocks decline, marine aquaculture is expected to play an increasing role in satisfying the global need for seafood. Since the expansion of near-shore aquaculture is becoming more difficult because of multi-use issues and environmental impact concerns, the feasibility of moving aquaculture into the open ocean is being studied. To enable the optimum design and evaluation of fish cage and mooring performance in the energetic open ocean, physical and numerical modeling techniques are being utilized. To validate these methods, the dynamics of a fish cage and mooring system deployed in the Gulf of Maine are simulated with physical and numerical models and compared with field observations. Assuming that the system can be modeled as a linear system, a stochastic approach was used to analyze the motion response (heave, surge and pitch) characteristics of the fish cage and the load (tension) response in an anchor line to wave forcing. Transfer functions were calculated from field observations for storm events and used to understand the system dynamics and to validate the models for the deployed system. Fish cage heave and surge motions were found to be overdamped, while pitch exhibited a resonance at low frequencies (less than 0.1 Hz). Transfer functions for anchor line tension were consistent with observations over most of the wave frequencies. The physical model clearly revealed the pitch resonance, while the numerical model was better at predicting mooring line tension. Results also provided insight concerning dynamical processes that require further study, including fluid–net panel interaction, transfer function amplitude dependence and the nonlinear relationship between steady current and wave fluid velocity on drag and its effect on system geometry and therefore response.

Dynamics of a supercooled polymer melt above themode-coupling critical temperature: cage versus polymer-specificeffects

This paper reports results of molecular dynamics simulations for aglassy polymer melt consisting of short, non-entangled chains. Thetemperature region studied covers the supercooled state of the meltabove the mode-coupling critical temperature. The analysis focuseson the interplay of simple-liquid and polymer-specific effects. Onecan clearly distinguish two regimes: a regime of small and one of largemonomer displacements. The first regime corresponds to motion of amonomer in its local environment. It is dominated by the cage effectand well described by the idealized mode-coupling theory. Thesecond regime is governed by the late-β/early-α process.In this regime the connectivity of the monomers begins tointerfere with the cage dynamics and finally becomes dominant. Themonomer displacement is compared with simulation results for abinary Lennard-Jones mixture to highlight the differences which areintroduced by the connectivity of the particles.

Cage Dynamics in the Third-Order Off-Resonant Response of Liquid Molecules: A Theoretical Realization

Abstract It is generally believed that the ultrafast initial spectroscopic response from the molecules in the condensed phase originates from small amplitude inertial motions within the cage formed by the nearest-neighbor solvent molecules surrounding the probe, or the cage effect. However, no quantitative estimate of this dynamics has been available for the currently popular experiments which measure the third-order off-resonant response. In this work, we fill this gap by a microscopic approach and demonstrate that the cage dynamics alone can produce the initial rise in the subpicosecond (ca. 200 fs) range in the third-order response. A simple analytical expression for the initial Gaussian time constant relevant to various kinds of the third-order off-resonant experiments is presented, which is found to be rather strongly dependent on the temperature. Connection with the non-polar solvation dynamics is also discussed.

Thermal mobility of atomic hydrogen in solid argon and krypton matrices

Decay patterns of atomic hydrogen trapped in argon and krypton matrices are followed by electron paramagnetic resonance (EPR). Hydrogen atoms are generated by uv-photolysis of HBr and HCl precursor molecules. The EPR signals due to interstitially trapped hydrogen atoms in octahedral sites disappear near 16 and 24 K in Ar and Kr, respectively. Substitutionally trapped H atoms are thermally stable up to evaporation temperature of the solids. The fate of thermally released H atoms in Ar is exclusively due to geminate recombination of the parent molecule. The observed kinetics is well fitted with double exponential decay. The kinetic behavior reflects short-range dissociation and recombination dynamics in Ar. In the Kr matrix, a change from first-order to second-order kinetics is observed at higher concentrations as formation of molecular hydrogen becomes important. From bimolecular decay kinetics, a diffusion constant of 4×10−15 cm2 s−1 is deduced for H-atom diffusion in Kr at 26.9 K. The obtained activation energies, 6–7 kJ/mol in Ar and 9–14 kJ/mol in Kr, are measures of thermally activated cage dynamics and show only weak dependence on the hydrogen isotope.

Mode coupling mechanisms in the impulsive 2D Raman response of liquid CS 2

The 2D Raman response of CS 2 is dominated by slow diffusive dynamics along the first propagation time while it is determined by ultrafast inertia-limited motions along the second time variable. These features cannot be explained when the reorientational diffusion and coherent intermolecular vibrations are modeled as independent processes. Mode coupling induced by the nonlinear polarizability can partly reproduce the observed asymmetry but yields wrong predictions at early times. Mode coupling by anharmonic interactions cannot even qualitatively account for the experimental data. An improved description of interaction-induced effects and cage dynamics is required for a better understanding of the 2D Raman response.