Insight into Local Structure and Molecular Dynamics in Organic Solid‐State Ionic Conductors

Elucidating the rate and geometry of molecular dynamics is particularly important for unravelling ion‐conduction mechanisms in electrochemical materials. The local molecular motions in the plastic crystal 1‐ethyl‐1‐methylpyrrolidinium tetrafluoroborate ([C₂mpyr][BF₄]) are studied by a combination of quantum chemical calculations and advanced solid‐state nuclear magnetic resonance spectroscopy. For the first time, a restricted puckering motion with a small fluctuation angle of 25° in the pyrrolidinium ring has been observed, even in the low‐temperature phase (?45 °C). This local molecular motion is deemed to be particularly important for the material to maintain its plasticity, and hence, its ion mobility at low temperatures.     

Molecular simulation of nanoclusters of gas hydrates in a water shell. The mechanical state of the system

The molecular dynamics method is employed to study hydrates of methane (sI), and krypton hydrate (sII), as well as an ice nanocluster in a supercooled water shell. The main attention is focused on the local structure and the mechanical state of two-phase nanosized systems, which is described using the local pressure tensor. Analysis of the temperature dependence of the local pressure allows one to compare two possible mechanisms responsible for the anomalous stability of gas hydrates at ambient pressure. According to the first mechanism, the water shell plays the role of a barrier that prevents the gas from escaping from the hydrate core. The second mechanism implies that the water shell generates additional pressure, which transfers the hydrate to a thermodynamically stable state. Results of molecular dynamics simulation indicate that both mechanisms are simultaneously involved in the stabilization of the hydrate nanocluster.     

High Pressure Induced Coil-Globule Transitions of Smart Polymers

Summary: In current work time-resolved optical spectroscopy (TROS) has been used to study coil-globule transitions monitored by the local segmental dynamics of anthracene labeled poly (N-isopropymethacrylamide), PNIPMAM as a function of pressure (0.1 MPa–200 MPa) over a temperature range of 283 K to 333 K. The positions of temperature-induced transition were observed to be independent on molecular weight of polymer at low pressures. The positions of pressure-induced transition were observed to be dependent on molecular weight of polymer at temperatures below LCST at atmospheric pressure. Double globule-coil-globule transition was observed to occur with pressure increasing at temperatures nearly above LCST. All these results along with values of intrinsic viscosity evaluated from values of correlation times measured for globules formed at different pressure/temperature conditions suggest the different mechanisms of compactisation governed by pressure and temperature and, correspondently, the different types of final structures. At low pressures with temperature increasing the compact, well-packed globules are forming via initial interactions between neighboring parts of polymer chain and further collapse. Relatively loosened particles are forming with pressurizing at low temperatures. Interaction between remote along the chain units takes part from the first stage of globule formation. And finally, rather solvated and irregularly twisted particles are forming at high pressure and high temperatures, i.e. at conditions, when both processes are involved.     

On effective potentials in classical mechanical systems

A classical mechanical variational method for computing effective potentials due to exact, first order and adiabatic constraints is presented. The effective potential can be used to envision in configuration space the restricted motion imposed by the constraints relative to the full potential. It can locate effective equilibrium structures and transition barriers and saddles and can be used when combined with semi-classical ideas to delineate regions of quantum packet flow and stationary state localization. The latter gives information on energy flow in a system and on the nature of basis sets needed for full quantum calculations. The advantage of the method is that is does not involve the solution of any equations of motion. The ideas are illustrated by some examples coming from the area of atomic and molecular dynamics.     

Atomistic investigation of segmental mobility in atactic poly(propylene)

An atomistic model previously developed for atactic poly(propylene) has been analyzed through molecular dynamics simulation to study the variation of static and dynamical properties across a temperature range centered around the experimental glass transition temperature. Although few effects are seen in structural measures such as chain conformation, shape, and packing, characteristic features associated with the onset of segmental motions are revealed in the simulation results on local dynamics. The mechanism by which the vinyl polymer chain undergoes thermally activated motion is found to involve a series of spatial displacement events (SDE) occurring topologically, spatially, and temporally in a discrete fashion. An attempt was made to correlate the motions of the active chain segments with structural and mechanical properties such as local volume and rotational stiffness. The results indicate that the ability of the segmental mobility to diffuse in space and time, in a dynamically percolative manner, is a significant feature of atomic motions in glassy polymers.     

Microphase separation and ion‐conduction mechanisms in polypropylene oxide/lithium perchlorate (LiClO4) complexes

Broadband dielectric spectroscopy was used to examine ion‐conduction mechanisms in polypropylene oxide (PPO) with a molecular weight of 4000 complexed with LiClO₄. Two distinct conduction mechanisms were proposed with respect to high and low salt concentration regions. In a concentrated regime (Li/O >10%), the segmental motion of PPO molecules is significantly slowed down by enhanced cation coordination that results in a marked decrease in molar conductivity. We found a linear relationship between the ionic diffusion coefficient and the relaxation frequency of slowed segmental motion over broad temperature and salt‐concentration ranges. The use of a random walk scheme revealed that ions hop around at the same rate as slowed segmental motion for a monomer length. In a dilute regime (Li/O <0.1%), ions are temporarily localized in a limited domain. The direct current conductivity is achieved by structural renewal that releases ions from such localization and provides a diffusional character. At intermediate salt concentrations, microphase separation into ion‐depleted and ion‐rich regions was evidenced by the coexistence of fast and slow segmental processes. The molar conductivity revealed a maximum at Li/O = 3%. Its decrease at higher salt concentrations was attributed to the slowing down of segmental motion, and that at lower salt concentrations was attributed to localization of ionic motion. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 613–622, 2002; DOI 10.1002/polb.10123     

Structural and dynamic features of water and amorphous ice

Structural properties and microscopic dynamics of water and amorphous ice have been studied by the molecular dynamics method. It has been found that the distribution function of the tetrahedricity parameter exhibits two ranges, which correspond to local molecular formations with low and high degrees of tetrahedricity. The number of molecular clusters with a high degree of tetrahedricity grows as temperature decreases. It has been shown that the vibrational density of states comprises two vibrational modes. A low-frequency vibrational mode strongly depends on pressure and is almost independent of temperature, while a high-frequency mode is relevant to the pressure-independent heat motion of molecules. The geometric criterion of hydrogen bonds has been used to evaluate their continuous lifetime as depending on temperature for molecules with different coordination values. The average lifetime of a hydrogen bond substantially depends on the coordination of molecules, with the temperature dependence of the coordination obeying the activation dynamics.     

An improved picture of methyl dynamics in proteins from slowly relaxing local structure analysis of 2H spin relaxation

Protein dynamics is intimately related to biological function. Core dynamics is usually studied with 2H spin relaxation of the 13CDH2 group, analyzed traditionally with the model-free (MF) approach. We showed recently that MF is oversimplified in several respects. This includes the assumption that the local motion of the dynamic probe and the global motion of the protein are decoupled, the local geometry is simple, and the local ordering is axially symmetric. Because of these simplifications MF has yielded a puzzling picture where the methyl rotation axis is moving rapidly with amplitudes ranging from nearly complete disorder to nearly complete order in tightly packed protein cores. Our conclusions emerged from applying to methyl dynamics in proteins the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Polimeno, A.; Freed, J. H. J. Phys. Chem. 1995, 99, 10995-11006.), which can be considered the generalization of MF, with all the simplifications mentioned above removed. The SRLS picture derived here for the B1 immunoglobulin binding domain of peptostreptococcal protein L, studied over the temperature range of 15-45 degrees C, is fundamentally different from the MF picture. Thus, methyl dynamics is characterized structurally by rhombic local potentials with varying symmetries and dynamically by tenfold slower rates of local motion. On average, potential rhombicity decreases, mode-coupling increases, and the rate of local motion increases with increasing temperature. The average activation energy for local motion is 2.0 +/- 0.2 kcal/mol. Mode-coupling affects the analysis even at 15 degrees C. The accuracy of the results is improved by including in the experimental data set relaxation rates associated with rank 2 coherences.     

Configurational temperature control for atomic and molecular systems

A new configurational temperature thermostat suitable for molecules with holonomic constraints is derived. This thermostat has a simple set of motion equations, can generate the canonical ensemble in both position and momentum space, acts homogeneously through the spatial coordinates, and does not intrinsically violate the constraints. Our new configurational thermostat is closely related to the kinetic temperature Nosé-Hoover thermostat with feedback coupled to the position variables via a term proportional to the net molecular force. We validate the thermostat by comparing equilibrium static and dynamic quantities for a fluid of n-decane molecules under configurational and kinetic temperature control. Practical aspects concerning the implementation of the new thermostat in a MOLECULAR DYNAMICS code and the potential applications are discussed.     

Dielectric relaxations in poly(vinylidene fluoride)

Molecular motions in poly(vinylidene fluoride) were studied by the dielectric technique. Three distinct absorption peaks (α_c, α_a, and β) were observed in the frequency range from 0.1 cps to 300 kcps and in the temperature range from ?66 to 100°C. The molecular mechanisms for these absorptions and their temperature dependence are discussed, and results are compared with x-ray diffraction and the NMR measurements. It is concluded that the α_c absorption located at 97°C (1 kcps) is related to molecular motion in the crystalline region. The α_a absorption located at ?27°C (1 kcps) can be interpreted as due to the micro-Brownian motion of the amorphous main chains. The β absorption located at ?47°C (1 kcps) is attributed to local oscillation of the frozen main chains.     

Simulation of liquid imidazole using a high-rank quantum topological electrostatic potential

Rigid body molecular dynamics simulations were carried out on pure liquid imidazole at four different temperatures and at 1 atm. Imidazole, which is important both in life science and materials science, is one of the simplest molecules to possess both a lone pair and a π system. These two features are known to benefit from multipolar electrostatics. Here the electrostatic interaction is governed by atomic multipole moments obtained from topologically partitioned ab initio electron densities. The non-electrostatic terms are modeled with Lennard-Jones parameters adjusted to fit the experimental liquid density. All σ values are incrementally increased by one single scaling factor. We report on how the presence of multipolar electrostatics influences the local structure, dynamics and thermodynamics of the liquid compared to electrostatics by atomic point charges. The point charge force field exaggerates the number of π-stacked dimers in the liquid, and underestimates the number of hydrogen-bonded dimers. The effect of the temperature on the local structure of liquid imidazole was analysed using radial and spatial distribution functions.     

Exploring the local conformational space of a membrane protein by site-directed spin labeling

Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function-structure relationship of membrane proteins.     

Geometry of phenylene motion in polycarbonate from NMR spectroscopy and neutron scattering

In view of the importance of molecular dynamics in condensed matter both time scale and geometry of such processes should be determined experimentally. Whereas many techniques are available for the former, only NMR spectroscopy and neutron scattering can provide detailed information on the latter. Because of the different time scales of the dynamics, which the two techniques can detect best, direct comparisons of probing the geometry of the dynamics in the same system are scarce. Here we present such a comparison for the complex rotational motion of the phenylene groups in amorphous polycarbonate based on published (2)H NMR and newly recorded (13)C NMR data covering a wide temperature range, and recent quasielastic neutron scattering (QENS) data. We show that the results of the two techniques are in remarkable agreement, provided the data are consistently analyzed. No evidence is found for additional motions characterized by 90 degrees flips recently deduced from QENS data alone. Instead, the phenylene motion in the glassy state displays a broad heterogeneous distribution of rotational angles, about 80 degrees in width, centered at a flip angle of 180 degrees , which stays essentially constant over a wide temperature range. Thus, the phenylene motion that can consistently be observed in NMR and neutron scattering experiments is sensitive to the local packing.     

Dielectric Relaxation of Type‐A Polymers in Melts and Solutions

This article describes the dielectric relaxation behavior of flexible polymer chains having the so‐called type‐A dipoles parallel along the chain backbone. This behavior reflects the global chain motion. Viscoelastically well known features of this motion, such as the power‐law relationship between the relaxation time and molecular weight of entangled linear chains (τ₁ ∝ M^3.5), are also observed dielectrically. More importantly, the dielectric behavior of linear chains having once‐inverted type‐A dipoles enables us to find some detailed dynamic features such as changes in the eigenfunctions f_p of a local correlation function with the chain concentration in solutions. These changes are discussed in relation to motional coupling of concentrated chains. The dielectric properties detect the orientational correlation of two submolecules in the chain at two separate times, while the viscoelastic properties reflect the isochronal orientational anisotropy of individual submolecules. Thus the chain motion is differently averaged in the dielectric and viscoelastic properties, and comparison of these properties enables us to find novel dynamic features. Specifically, this comparison reveals the validity of the tube dilation molecular picture for entangled linear chains and weakening of the short‐time coherence of the submolecule motion due to the constraint release mechanism. Moreover, the dielectric method enables us to investigate the chain dynamics under strong flow and/or in a molecularly narrow space. In particular, the retarded dielectric relaxation found for homopolymers and block copolymers in such narrow spaces (in the microdomains for the latter) indicates important effects of the spatial and thermodynamic constraints on the global chain motion. All the above results in turn demonstrate the importance of the dielectric method in investigations of the polymer dynamics.     

温控分子动力学研究微管蛋白活性肽链的折叠机制

运用温控和常温分子动力学方法, 研究了微管蛋白活性部位Pep1-28肽链的折叠机制, 总模拟时间为380.0 ns. 对于温控分子动力学, 逐渐降温可以清晰显示Pep1-28肽链的折叠途径, 发生明显折叠的温度约为550 K, 其折叠和去折叠可逆机制为U(>1200 K)←→I1(1200-1000 K)←→I2(800 K)←→I3(600 K)←→I4(450 K)←→F1(400 K)←→F2(300 K), 其中U为去折叠态构象, I1、I2、I3和I4是折叠过程中的四个重要的中间态构象, F1和F2是两个结构相近的折叠态构象. 对于常温(300 K)分子动力学, 其构象转变和折叠过程相当迅速, 很难观察到有效、稳定的中间态构象. 尤其引人注意的是, 其折叠态结构陷入了能量局域极小点, 与温控(300 K)的有较大差异, 两者能量差高达297.53 kJ·mol-1. 可见, 温控分子动力学方法不仅清晰地显示多肽和蛋白质折叠过程的重要中间态构象, 为折叠和去折叠机制提供直接、可靠的依据, 而且还有助于跨越较高的构象能垒, 促使多肽和蛋白质折叠以形成全局能量最低的稳定结构.     

Long-time overdamped Langevin dynamics of molecular chains

We present a novel algorithm of constrained, overdamped dynamics to study the long-time properties of peptides, proteins, and related molecules. The constraints are applied to an all-atom model of the molecule by projecting out all components of the nonbonding interactions which tend to alter fixed bond lengths and angles. Because the overdamped dynamical equations are first order in time, the constraints are satisfied by inversion of a banded matrix at each timestep, which is computationally efficient. Thermal effects are included through a Langevin noise term in the equation of motion. Because high-frequency components of the motion have been eliminated, the timestep of the algorithm is determined by the nonbonding forces, which are two to three orders of magnitude weaker than the bonding forces. Using polyalanine as a test example, we demonstrate that trajectories simulating a microsecond of motion can be run about 10³ times faster than an equivalent molecular dynamics simulation. © 1994 by John Wiley & Sons, Inc.     

Investigating the relationship between infrared spectra of shared protons in different chemical environments: a comparison of protonated diglyme and protonated water dimer

The energetics, dynamics, and infrared spectroscopy of the shared proton in different chemical environments is investigated using molecular dynamics simulations. A three-dimensional potential energy surface (PES) suitable for describing proton transfer between an acceptor and a donor oxygen atom is combined with an all-atom force field to carry out reactive molecular dynamics simulations. The construction of the fully dimensional PES is inspired from the established mixed quantum mechanics/molecular mechanics treatment of larger systems. The "morphing potential" method is used to transform the generic PES for proton transfer along an O...H+...O motif into a three-dimensional PES for proton transfer in protonated diglyme. Using molecular dynamics simulations at finite temperature, the gas phase infrared spectra are calculated for both species from the Fourier transform of the dipole moment autocorrelation function. For protonated diglyme the modes involving the H+ motion are strongly mixed with other degrees of freedom. At low temperature, the O...H+...O asymmetric stretching vibration is found at 870 cm-1, whereas for H5O2+ this band is at 724 cm-1. As expected, the vibrational bands of protonated diglyme show no temperature dependence whereas for H5O2+ at T = 100 K the proton transfer mode is found at 830 cm-1, in good agreement with 861 cm-1 from very recent molecular dynamics simulations.     

Rotational flexibility in NH4+-encapsulated 18-crown-6 studied by molecular dynamics and positron annihilation: where does the positron localize?

Conformational flexibility of the ammonium complex of macrocyclic 18-crown-6 at 100 K < or = T < or = 300 K is studied using a positron microprobe in conjunction with molecular dynamics simulations. The ammonium cation, encapsulated in a three-pointed hydrogen-bonding perching arrangement, undergoes unhindered facile rotation inside the crown cavity, and the ether backbone adopts itself to the dynamic cation conformation. Preferential localization of the positron in the vicinity of the encapsulated cation results in the positron sensing changes in the local electron density distribution arising from the unrestricted rotational motion of the cation as well as from the slow motion of the crown backbone and hence sensing only an average conformation of the complex.     

A configurational temperature Nosé-Hoover thermostat

We propose two new thermostats which can be employed in computer simulations to ensure that two different variants of the configurational temperature fluctuate around their equilibrium values. These new thermostats differ from one previously introduced by Delhommelle and Evans [Mol. Phys. 99, 1825 (2001)] in several important ways. First, our thermostats are derived in the same spirit as the Nosé-Hoover thermostat and therefore generate the canonical phase-space distribution. Second, our thermostats involve simpler equations of motion, which do not involve spatial gradients of the configurational temperature. They do not suffer from problems stemming from stiff equations of motion and furthermore, in large temperature perturbation simulations, the measured temperature follows the set-point temperature without any overshoot, and with good damping of oscillations. We show that both of our configurational thermostats are special cases of a more general set of Nosé-Hoover equations proposed by Kusnezov et al. [Ann. Phys. 204, 155 (1990)]. The new thermostats are expected to be highly useful in nonequilibrium simulations, particularly those characterized by spatial inhomogeneities. They should also find applicability in simulations involving large changes in temperature over small time scales, such as temperature quench molecular dynamics and radiation damage modeling.     

Solvation dynamics in reverse micelles: the role of headgroup-solute interactions

We present molecular dynamics simulation results for solvation dynamics in the water pool of anionic-surfactant reverse micelles (RMs) of varying water content, w(0). The model RMs are designed to represent water/aerosol-OT/oil systems, where aerosol-OT is the common name for sodium bis(2-ethylhexyl)sulfosuccinate. To determine the effects of chromophore-headgroup interactions on solvation dynamics, we compare the results for charge localization in model ionic diatomic chromophores that differ only in charge sign. Electronic excitation in both cases is modeled as charge localization on one of the solute sites. We find dramatic differences in the solvation responses for anionic and cationic chromophores. Solvation dynamics for the cationic chromophore are considerably slower and more strongly w(0)-dependent than those for the anionic chromophore. Further analysis indicates that the difference in the responses can be ascribed in part to the different initial locations of the two chromophores relative to the surfactant interface. In addition, slow motion of the cationic chromophore relative to the interface is the main contributor to the longer-time decay of the solvation response to charge localization in this case.