Tuning the polymer thermal conductivity through structural modification induced by MoS2 bilayers.

The present work refers to a physical and structural study of nanoconfined polymers in polymer-MoS2 nanocomposites as a function of MoS2-MoS2 interlayer distance. We applied reverse nonequilibrium molecular dynamics (RNEMD) simulations to investigate the thermal conductivity (λ) of polyamide oligomers confined by MoS2 bilayers. The results of this study indicate that thermal conductivity of polymer can be considerably enhanced when polymer chains are confined by MoS2 sheets, this behavior is more pronounced by charged surfaces. The presence of MoS2 surfaces leads to elongation as well as preferential alignment of polymer chains parallel to the MoS2 surfaces, which in turn results in higher order and denser packing of polymer content and hence larger thermal conductivity in comparison to the bulk polymer. Additionally, the analysis of the number of hydrogen bonds (HBs) in confined polymer chains suggests that a combined effect of the mentioned structural modification and enlarged values of HBs may cooperatively contribute to high polymer thermal conductivity, facilitating phonon transport. The results reported here suggest a significant way to design confined polymer-MoS2 composites for significantly improving thermal conductivity for a wide variety of applications.

The complexin C-terminal amphipathic helix stabilizes the fusion pore open state by sculpting membranes.

Neurotransmitter release is mediated by proteins that drive synaptic vesicle fusion with the presynaptic plasma membrane. While soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs) form the core of the fusion apparatus, additional proteins play key roles in the fusion pathway. Here, we report that the C-terminal amphipathic helix of the mammalian accessory protein, complexin (Cpx), exerts profound effects on membranes, including the formation of pores and the efficient budding and fission of vesicles. Using nanodisc-black lipid membrane electrophysiology, we demonstrate that the membrane remodeling activity of Cpx modulates the structure and stability of recombinant exocytic fusion pores. Cpx had particularly strong effects on pores formed by small numbers of SNAREs. Under these conditions, Cpx increased the current through individual pores 3.5-fold, and increased the open time fraction from roughly 0.1 to 1.0. We propose that the membrane sculpting activity of Cpx contributes to the phospholipid rearrangements that underlie fusion by stabilizing highly curved membrane fusion intermediates.

Benchmarking the Performance of the ReaxFF Reactive Force Field on Hydrogen Combustion Systems.

A thorough understanding of the kinetics and dynamics of combusting mixtures is of considerable interest, especially in regimes beyond the reach of current experimental validation. The ReaxFF reactive force field method has provided a way to simulate large-scale systems of hydrogen combustion via a parametrized potential that can simulate bond breaking. This modeling approach has been applied to hydrogen combustion, as well as myriad other reactive chemical systems. In this work, we benchmark the performance of several common parametrizations of this potential against higher-level quantum mechanical (QM) approaches. We demonstrate instances where these parametrizations of the ReaxFF potential fail both quantitatively and qualitatively to describe reactive events relevant for hydrogen combustion systems.

Effects of temperature and mass conservation on the typical chemical sequences of hydrogen oxidation.

Macroscopic properties of reacting mixtures are necessary to design synthetic strategies, determine yield, and improve the energy and atom efficiency of many chemical processes. The set of time-ordered sequences of chemical species are one representation of the evolution from reactants to products. However, only a fraction of the possible sequences is typical, having the majority of the joint probability and characterizing the succession of chemical nonequilibrium states. Here, we extend a variational measure of typicality and apply it to atomistic simulations of a model for hydrogen oxidation over a range of temperatures. We demonstrate an information-theoretic methodology to identify typical sequences under the constraints of mass conservation. Including these constraints leads to an improved ability to learn the chemical sequence mechanism from experimentally accessible data. From these typical sequences, we show that two quantities defining the variational typical set of sequences-the joint entropy rate and the topological entropy rate-increase linearly with temperature. These results suggest that, away from explosion limits, data over a narrow range of thermodynamic parameters could be sufficient to extrapolate these typical features of combustion chemistry to other conditions.

Nonexponential kinetics of ion pair dissociation in electrofreezing water.

Temporally- or spatially-heterogeneous environments can participate in many kinetic processes, from chemical reactions and self-assembly to the forced dissociation of biomolecules. Here, we simulate the molecular dynamics of a model ion pair forced to dissociate in an explicit, aqueous solution. Triggering dissociation with an external electric field causes the surrounding water to electrofreeze and the ion pair population to decay nonexponentially. To further probe the role of the aqueous environment in the kinetics, we also simulate dissociation events under a purely mechanical force on the ion pair. In this case, regardless of whether the surrounding water is a liquid or already electrofrozen, the ion pair population decays exponentially with a well-defined rate constant that is specific to the medium and applied force. These simulation data, and the rate parameters we extract, suggest the disordered kinetics in an electrofreezing medium are a result of the comparable time scales of two concurrent processes, electrofreezing and dissociation.

Nonequilibrium phase coexistence and criticality near the second explosion limit of hydrogen combustion.

While hydrogen is a promising source of clean energy, the safety and optimization of hydrogen technologies rely on controlling ignition through explosion limits: pressure-temperature boundaries separating explosive behavior from comparatively slow burning. Here, we show that the emergent nonequilibrium chemistry of combustible mixtures can exhibit the quantitative features of a phase transition. With stochastic simulations of the chemical kinetics for a model mechanism of hydrogen combustion, we show that the boundaries marking explosive domains of kinetic behavior are nonequilibrium critical points. Near the pressure of the second explosion limit, these critical points terminate the transient coexistence of dynamical phases-one that autoignites and another that progresses slowly. Below the critical point temperature, the chemistry of these phases is indistinguishable. In the large system limit, the pseudo-critical temperature converges to the temperature of the second explosion limit derived from mass-action kinetics.

Ignition in an Atomistic Model of Hydrogen Oxidation.

Hydrogen is a potential substitute for fossil fuels that would reduce the combustive emission of carbon dioxide. However, the low ignition energy needed to initiate oxidation imposes constraints on the efficiency and safety of hydrogen-based technologies. Microscopic details of the combustion processes, ephemeral transient species, and complex reaction networks are necessary to control and optimize the use of hydrogen as a commercial fuel. Here, we report estimates of the ignition time of hydrogen-oxygen mixtures over a wide range of equivalence ratios from extensive reactive molecular dynamics simulations. These data show that the shortest ignition time corresponds to a fuel-lean mixture with an equivalence ratio of 0.5, where the number of hydrogen and oxygen molecules in the initial mixture are identical, in good agreement with a recent chemical kinetic model. We find two signatures in the simulation data precede ignition at pressures above 200 MPa. First, there is a peak in hydrogen peroxide that signals ignition is imminent in about 100 ps. Second, we find a strong anticorrelation between the ignition time and the rate of energy dissipation, suggesting the role of thermal feedback in stimulating ignition.

Learning the mechanisms of chemical disequilibria.

When at equilibrium, large-scale systems obey thermodynamics because they have microscopic configurations that are typical. "Typical" states are a fraction of those possible with the majority of the probability. A more precise definition of typical states underlies the transmission, coding, and compression of information. However, this definition does not apply to natural systems that are transiently away from equilibrium. Here, we introduce a variational measure of typicality and apply it to atomistic simulations of a model for hydrogen oxidation. While a gaseous mixture of hydrogen and oxygen combusts, reactant molecules transform through a variety of ephemeral species en route to the product, water. Out of the exponentially growing number of possible sequences of chemical species, we find that greater than 95% of the probability concentrates in less than 1% of the possible sequences. Overall, these results extend the notion of typicality across the nonequilibrium regime and suggest that typical sequences are a route to learning mechanisms from experimental measurements. They also open up the possibility of constructing ensembles for computing the macroscopic observables of systems out of equilibrium.

Reactive symbol sequences for a model of hydrogen combustion.

Transient, macroscopic states of chemical disequilibrium are born out of the microscopic dynamics of molecules. As a reaction mixture evolves, the temporal patterns of chemical species encodes some of this dynamical information, while their statistics are a manifestation of the bulk kinetics. Here, we define a chemically-informed symbolic dynamics as a coarse-grained representation of classical molecular dynamics, and analyze the sequences of chemical species for a model of hydrogen combustion. We use reactive molecular dynamics simulations to generate the sequences and derive probability distributions for sequence observables: the reaction time scales and the chain length - the total number of reactions between initiation of a reactant and termination at products. The time scales and likelihood of the sequences depend strongly on the chain length, temperature, and density. Temperature suppresses the uncertainty in chain length for hydrogen sequences, but enhances the uncertainty in oxygen sequence chain lengths. This method of analyzing a surrogate chemical symbolic dynamics reduces the complexity of the chemistry from the atomistic to the molecular level and has the potential for extension to more complicated reaction systems.

Interfacial thermal transport and structural preferences in carbon nanotube-polyamide-6,6 nanocomposites: how important are chemical functionalization effects?

We employ reverse nonequilibrium molecular dynamics simulations to investigate the interfacial heat transfer in composites formed by an ungrafted or a grafted carbon nanotube which is surrounded by oligomeric polyamide-6,6 chains. The structural properties of the polymer matrix and the grafted chains are also studied. The influence of the grafting density, the length of the grafted chains as well as their chemical composition on the interfacial thermal conductivity (λi) are in the focus of our computational study. For the considered grafted polyethylene and polyamide chains we do not find a sizeable difference in the observed λi values. In contrast to this insensitivity, we predict a rather strong influence on λi by the grafting density and the length of the grafted chains. This dependence is an outcome of modifications in the structural properties of the polymer matrix as well as the grafted chains. Functionalization of the nanotube has a sizeable influence on the interfacial thermal conductivity. Its enhancement is caused by the chemical bonds between the nanotube and grafted chain atoms which reduce the number of Kapitza resistances hindering the heat transfer in polymer samples. The phonon density of states profiles confined to the bonded nanotube and the grafted chain atoms are used to emphasize the phonon support of the thermal conductivity in nanocomposites with grafted tubes. Strategies to tailor nanotube containing composites with higher thermal conductivities than that realized in the bare polymer are shortly touched.

Almost enclosed buckyball joints: synthesis, complex formation, and computational simulations of pentypticene-extended tribenzotriquinacene.

We report the synthesis of a tribenzotriquinacene-based (TBTQ) receptor (3) for C60 fullerene, which is extended by pentiptycene moieties to provide an almost enclosed concave ball bearing. The system serves as a model for a self-assembling molecular rotor with a flexible and adapting stator. Unexpectedly, nuclear magnetic resonance spectroscopic investigations reveal a surprisingly low complex stability constant of K1 =213±37 M(-1) for [C60 ⊂3], seemingly inconsistent with the previously reported TBTQ systems. Molecular dynamics (MD) simulations have been conducted for three different [C60 ⊂TBTQ] complexes to resolve this. Because of the dominating dispersive interactions, the binding energies increase with the contact area between guest and host, however, only for rigid host structures. By means of free-energy calculations with an explicit solvent model it can be shown that the novel flexible TBTQ receptor 3 binds weakly because of hampering entropic contributions.

Tribenzotriquinacene receptors for C60 †fullerene rotors: towards C3 symmetrical chiral stators for unidirectionally operating nanoratchets.

The synthesis of a stereochemically pure concave tribenzotriquinacene receptor (7) for C60 fullerene, possessing C3 point group symmetry, by threefold condensation of C2 -symmetric 1,2-diketone synthons (5) and a hexaaminotribenzotriquinacene core (6) is described. The chiral diketone was synthesized in a five-step reaction sequence starting from C2h -symmetric 2,6-di-tert-butylanthracene. The highly diastereo-discriminating Diels-Alder reaction of 2,6-di-tert-butylanthracene with fumaric acid di(-)menthyl ester, catalyzed by aluminium chloride, is the relevant stereochemistry introducing step. The structure of the fullerene receptor was verified by (1)H and (13)C NMR spectroscopy, mass spectrometry and single crystal X-ray diffraction. VCD and ECD spectra were recorded, which were corroborated by ab initio DFT calculations, establishing the chiral nature of 7 with about 99.7 % ee, based on the ee (99.9 %) of the chiral synthon (1). The absolute configuration of 7 could thus be established as all-S [(2S,7S,16S,21S,30S,35S)-(7)]. Spectroscopic titration experiments reveal that the host forms 1:1 complexes with either pure fullerene (C60) or fullerene derivatives, such as rotor 1'-(4-nitrophenyl)-3'-(4-N,N-dimethylaminophenyl)-pyrazolino[4',5':1,2][60]fullerene (R). The complex stability constants of the complexes dissolved in CHCl3/CS2 (1:1 vol. %) are K([C60 ⊂7]) = 319(±156) M(-1) and K([R⊂7]) = 110(±50) M(-1). With molecular dynamics simulations using a first-principles parameterized force field the asymmetry of the rotational potential for [R⊂7] was shown, demonstrating the potential suitability of receptor 7 to act as a stator in a unidirectionally operating nanoratchet.

Transversal thermal transport in single-walled carbon nanotube bundles: influence of axial stretching and intertube bonding.

Using reverse nonequilibrium molecular dynamics simulations the influence of intermolecular bridges on the thermal conductivity (λ) in carbon nanotube (CNT) bundles has been investigated. The chosen cross linkers (CH2, O, CO) strengthen the transversal energy transport relative to the one in CNT bundles without bridges. The results showed that λ does not increase linearly with the linker density. The efficiency of the heat transport is determined by the number of linkers in the direction of the heat flux, the type of the linker, and their spatial ordering. The influence of a forced axial stress on the transversal λ has been also studied. The observed λ reduction with increasing axial stretching in a neat CNT bundle can be (over)compensated by cross linkers. The present computational data emphasize the contribution of phonons to the transversal heat transport in CNT bundles with intertube bonds.

Thermal conductivity of carbon nanotube-polyamide-6,6 nanocomposites: reverse non-equilibrium molecular dynamics simulations.

The thermal conductivity of composites of carbon nanotubes and polyamide-6,6 has been investigated using reverse non-equilibrium molecular dynamics simulations in a full atomistic resolution. It is found, in line with experiments, that the composites have thermal conductivities, which are only moderately larger than that of pure polyamide. The composite conductivities are orders of magnitude less than what would be expected from naïve additivity arguments. This means that the intrinsic thermal conductivities of isolated nanotubes, which exceed the best-conducting metals, cannot be harnessed for heat transport, when the nanotubes are embedded in a polymer matrix. The main reason is the high interfacial thermal resistance between the nanotubes and the polymer, which was calculated in addition to the total composite thermal conductivity as well as that of the subsystem. It hinders heat to be transferred from the slow-conducting polymer into the fast-conducting nanotubes and back into the polymer. This interpretation is in line with the majority of recent simulation works. An alternative explanation, namely, the damping of the long-wavelength phonons in nanotubes by the polymer matrix is not supported by the present calculations. These modes provide most of the polymers heat conduction. An additional minor effect is caused by the anisotropic structure of the polymer phase induced by the nearby nanotube surfaces. The thermal conductivity of the polymer matrix increases slightly in the direction parallel to the nanotubes, whereas it decreases perpendicular to it.

Correlation between thermal conductivity and bond length alternation in carbon nanotubes: a combined reverse nonequilibrium molecular dynamics--crystal orbital analysis.

The thermal conductivity (λ) of carbon nanotubes (CNTs) with chirality indices (5,0), (10,0), (5,5), and (10,10) has been studied by reverse nonequilibrium molecular dynamics (RNEMD) simulations as a function of different bond length alternation patterns (Δr(i) ). The Δr(i) dependence of the bond force constant (k(rx) ) in the molecular dynamics force field has been modeled with the help of an electronic band structure approach. These calculations show that the Δr(i) dependence of k(rx) in tubes with not too small a diameter can be mapped by a simple linear bond length-bond order correlation. A bond length alternation with an overall reduction in the length of the nanotube causes an enhancement of λ, whereas an alternation scheme leading to an elongation of the tube is coupled to a decrease of the thermal conductivity. This effect is more pronounced in carbon nanotubes with larger diameters. The formation of a polyene-like structure in the direction of the longitudinal axis has a negligible influence on λ. A comparative analysis of the RNEMD and crystal orbital results indicates that Δr(i) -dependent modifications of λ and the electrical conductivity are uncorrelated. This behavior is in-line with a heat transfer that is not carried by electrons. Modifications of λ as a function of the bond alternation in the (10,10) nanotube are explained with the help of power spectra, which provide access to the density of vibrational states. We have suggested longitudinal low-energy modes in the spectra that might be responsible for the Δr(i) dependence of λ.

Thermal rectification in mass-graded nanotubes: a model approach in the framework of reverse non-equilibrium molecular dynamics simulations.

The thermal rectification in nanotubes with a mass gradient is studied by reverse non-equilibrium molecular dynamics simulations. We predict a preferred heat flow from light to heavy atoms which differs from the preferential direction in one-dimensional monoatomic systems. This behavior of nanotubes is explained by anharmonicities caused by transverse motions which are stronger at the low-mass end. The present simulations show an enhanced rectification with increasing tube length, diameter and mass gradient. Implications of the present findings for applied topics are mentioned concisely.

Anisotropy of the thermal conductivity of stretched amorphous polystyrene in supercritical carbon dioxide studied by reverse nonequilibrium molecular dynamics simulations.

The thermal conductivity (lambda) of stretched amorphous atactic polystyrene (PS) swollen in supercritical carbon dioxide (sc CO(2)) has been investigated over a wide temperature, pressure, and concentration range. Nonequilibrium molecular dynamics simulations with a full atomistic force-field have been employed to calculate the thermal conductivity of neat stretched PS and of different mixtures of supercritical CO(2) with stretched PS. As the energy transport in PS parallel and perpendicular to the stretching direction differs, an anisotropy in the thermal conductivity occurs. The magnitude of lambda is enhanced with an increasing number of carbon-carbon backbone bonds oriented parallel to the direction of the heat transport. The degrees of freedom in the side chain of the polymer are rather unimportant for the thermal conductivity. To understand the conditions leading either to an equivalence or nonequivalence of the system degrees of freedom for the heat transport, we have analyzed lambda of PS, CO(2), binary PS-CO(2) mixtures and other model systems as a function of the bond constraints in the computational model. Furthermore, we have commented on differences in the thermal conductivity provided either by a vibrational energy transfer or by collisions.

Thermal conductivity of amorphous polystyrene in supercritical carbon dioxide studied by reverse nonequilibrium molecular dynamics simulations.

The thermal conductivity of amorphous atactic polystyrene (PS) swollen in supercritical carbon dioxide (sc CO(2)) has been investigated over wide temperature, pressure, and concentration ranges. Nonequilibrium molecular dynamics simulations with a full atomistic force field have been used to calculate the thermal conductivity of neat PS and sc CO(2) as well as of the binary system at different compositions. An analytical interpolation formula for the thermal conductivity of the binary mixture on the basis of PS and CO(2) data has been obtained. Particular attention has been paid to the implications of the quasi-degeneracy and finite-size effects in the simulated polymer system. It has been found that, in addition to the degrees of freedom per volume, the orientation of the carbon-carbon bonds in the backbone relative to the direction of the temperature gradient is important for the heat transport in PS.

The thermal conductivity and thermal rectification of carbon nanotubes studied using reverse non-equilibrium molecular dynamics simulations.

The thermal conductivity of single-walled and multi-walled carbon nanotubes has been investigated as a function of the tube length L, temperature and chiral index using non-equilibrium molecular dynamics simulations. In the ballistic-diffusive regime the thermal conductivity follows a L(alpha) law. The exponent alpha is insensitive to the diameter of the carbon nanotube; alpha approximately 0.77 has been derived for short carbon nanotubes at room temperature. The temperature dependence of the thermal conductivity shows a peak before falling at higher temperatures (>500 K). The phenomenon of thermal rectification in nanotubes has been investigated by gradually changing the atomic mass in the tube-axial direction as well as by loading extra masses on the terminal sites of the tube. A higher thermal conductivity occurs when heat flows from the low-mass to the high-mass region.