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arXiv2014

The electric double layer has a life of its own

Using molecular dynamics simulations with recently developed importance sampling methods, we show that the differential capacitance of a model ionic liquid based double-layer capacitor exhibits an anomalous dependence on the applied electrical potential. Such behavior is qualitatively incompatible with standard mean-field theories of the electrical double layer, but is consistent with observations made in experiment. The anomalous response results from structural changes induced in the interfacial region of the ionic liquid as it develops a charge density to screen the charge induced on the electrode surface. These structural changes are strongly influenced by the out-of-plane layering of the electrolyte and are multifaceted, including an abrupt local ordering of the ions adsorbed in the plane of the electrode surface, reorientation of molecular ions, and the spontaneous exchange of ions between different layers of the electrolyte close to the electrode surface. The local ordering exhibits signatures of a first-order phase transition, which would indicate a singular charge-density transition in a macroscopic limit.

physics.chem-ph↗

arXiv2014

Polymer Nanofibers with Outstanding Thermal Conductivity and Thermal Stability: Fundamental Linkage between Molecular Characteristics and Macroscopic Thermal Properties

Polymer nanofibers with high thermal conductivities and outstanding thermal stabilities are highly desirable in heat transfer-critical applications such as thermal management, heat exchangers and energy storage. In this work, we unlock the fundamental relations between the thermal conductivity and thermal stability of polymer nanofibers and their molecular characteristics by studying the temperature-induced phase transitions and thermal transport of a series of polymer nanofibers. Ten different polymer nanofibers with systematically chosen molecular structures are studied using large scale molecular dynamics simulations. We found that high thermal conductivity and good thermal stability can be achieved in polymers with rigid backbones, exemplified by π-conjugated polymers, due to suppressed segmental rotations and large phonon group velocities. The low probability of segmental rotation does not only prevent temperature-induced phase transition but also enables long phonon mean free paths due to reduced disorder scattering. Although stronger inter-chain interactions can also improve the thermal stability, polymers with such a feature usually have heavier atoms, weaker backbone bonds, and segments vulnerable to random rotations, which lead to low thermal conductivities. This work elucidates the underlying linkage between the molecular nature and macroscopic thermal properties of polymer nanofibers, which is instrumental to the design of thermally conductive polymer nanofibers with high temperature stabilities.

physics.chem-ph↗

arXiv2014

Weak self-interactions of globular proteins studied by small-angle X-ray scattering and structure-based modeling

We investigate protein-protein interactions in solution by small-angle X-ray scattering (SAXS) and theoretical modeling. The structure factor for solutions of bovine pancreatic trypsin inhibitor (BPTI), myoglobin (Mb), and intestinal fatty acid-binding protein (IFABP) is determined from SAXS measurements at multiple concentrations, from Monte Carlo simulations with a coarse-grained structure-based interaction model, and from analytic approximate solutions of two idealized colloidal interaction models without adjustable parameters. By combining these approaches, we find that the structure factor is essentially determined by hard-core and screened electrostatic interactions. Other soft short-ranged interactions (van der Waals and solvation-related) are either individually insignificant or tend to cancel out. The structure factor is also not significantly affected by charge fluctuations. For Mb and IFABP, with small net charge and relatively symmetric charge distribution, the structure factor is well described by a hard-sphere model. For BPTI, with larger net charge, screened electrostatic repulsion is also important, but the asymmetry of the charge distribution reduces the repulsion from that predicted by a charged hard-sphere model with the same net charge. Such charge asymmetry may also amplify the effect of shape asymmetry on the protein-protein potential of mean force.

physics.bio-ph↗

arXiv2014

Range separated hybrid density functional study of organic dye sensitizers on anatase TiO$_2$ nanowires

The adsorption of organic molecules coumarin and the donor-$π$-acceptor type tetrahydroquinoline (C2-1) on anatase (101) and (001) nanowires have been investigated using screened Coulomb hybrid density functional theory calculations. While coumarin forms single bond with the nanowire surface, C2-1 additionally exhibits bidentate mode giving rise to much stronger adsorption energies. Nonlinear solvation effects on the binding characteristics of the dye chromophores on the nanowire facets have also been examined. These two dye sensitizers show different electronic charge distributions for the highest occupied and the lowest unoccupied molecular states. We studied the electronic structures in terms of the positions of the band edges and adsorbate related band gap states and their effect on the absorption spectra of the dye-nanowire combined systems. These findings were interpreted and discussed from the view point of better light harvesting and charge separation as well as in relation to more efficient charge carrier injection into the semiconductor nanowire.

cond-mat.mes-hall↗

arXiv2014

Charge relaxation dynamics of an electrolytic nanocapacitor

Understanding ion relaxation dynamics in overlapping electric double layers (EDLs) is critical for the development of efficient nanotechnology based electrochemical energy storage, electrochemomechanical energy conversion and bioelectrochemical sensing devices as well as controlled synthesis of nanostructured materials. Here, a Lattice Boltzmann (LB) method is employed to simulate an electrolytic nanocapacitor subjected to a step potential at t = 0 for various degrees of EDL overlap, solvent viscosities, ratios of cation to anion diffusivity and electrode separations. The use of a novel, continuously varying and Galilean invariant, molecular speed dependent relaxation time (MSDRT) with the LB equation recovers a correct microscopic description of the molecular collision phenomena and enhances the stability of the LB algorithm. Results for large EDL overlaps indicated oscillatory behavior for the ionic current density in contrast to monotonic relaxation to equilibrium for low EDL overlaps. Further, at low solvent viscosities and large EDL overlaps, anomalous plasma-like spatial oscillations of the electric field were observed that appeared to be purely an effect of nanoscale confinement. Employing MSDRT in our simulations enabled a modeling of the fundamental physics of the transient charge relaxation dynamics in electrochemical systems operating away from equilibrium wherein Nernst-Einstein relation is known to be violated.

physics.chem-ph↗

arXiv2014

Quantum effects in the diffusion of hydrogen on Ru(0001)

An understanding of hydrogen diffusion on metal surfaces is important, not just for its role in heterogeneous catalysis and hydrogen fuel cell technology, but also because it provides model systems where tunneling can be studied under well-defined conditions. Here we report helium spin-echo measurements of the atomic-scale motion of hydrogen on the Ru(0001) surface between 75 and 250 K. Quantum effects are evident at temperatures as high as 200 K, while below 120 K we observe a tunneling-dominated temperature independent jump rate of 1.9$\times$10$^9$ s$^{-1}$, many orders of magnitude faster than previously seen. Quantum transition state theory calculations based on ab initio path-integral simulations reproduce the temperature dependence of the rate at higher temperatures and predict a crossover to tunneling-dominated diffusion at low temperatures, although the tunneling rate is under-estimated, highlighting the need for future experimental and theoretical studies of hydrogen diffusion on well-defined surfaces.

physics.chem-ph↗

arXiv2013

Clustered Geometries Exploiting Quantum Coherence Effects for Efficient Energy Transfer in Light Harvesting

Elucidating quantum coherence effects and geometrical factors for efficient energy transfer in photosynthesis has the potential to uncover non-classical design principles for advanced organic materials. We study energy transfer in a linear light-harvesting model to reveal that dimerized geometries with strong electronic coherences within donor and acceptor pairs exhibit significantly improved efficiency, which is in marked contrast to predictions of the classical Förster theory. We reveal that energy tuning due to coherent delocalization of photoexcitations is mainly responsible for the efficiency optimization. This coherence-assisted energy-tuning mechanism also explains the energetics and chlorophyll arrangements in the widely-studied Fenna-Matthews-Olson complex. We argue that a clustered network with rapid energy relaxation among donors and resonant energy transfer from donor to acceptor states provides a basic formula for constructing efficient light-harvesting systems, and the general principles revealed here can be generalized to larger systems and benefit future innovation of efficient molecular light-harvesting materials.

physics.bio-ph↗

arXiv2014

The penetration barrier of water through graphynes' pores: first-principles predictions and force field optimization

Graphynes are novel two-dimensional carbon-based materials that -due to their nanoweb-like structure- have been proposed as molecular filters, especially for water purification technologies. In this work we carry out first principles electronic structure calculations at the MP2C level of theory to assess the interaction between water and graphyne, graphdiyne and graphtriyne pores. The computed penetration barriers suggest that water transport is unfeasible through graphyne while being unimpeded for graphtriyne. Nevertheless, for graphdiyne, which presents a pore size almost matching that of water, a low barrier is found which in turn disappears if an active hydrogen bond with an additional water molecule on the opposite side of the opening is taken into account. These results support the possibility of using graphtriyne as an efficient membrane for water filtration but, in contrast with previous determinations, they do not exclude graphdiyne. In fact, the related first principles penetration barrier leads to water permeation probabilities which are at least two order of magnitude larger than those estimated by employing commonly used force fields. A new pair potential for the water--carbon non-covalent component of the interaction has been built and it is recommended for molecular dynamics simulation involving graphdiyne and water.

physics.chem-ph↗

arXiv2014

Unveiling the Surface Structure of Amorphous Solid Water via Selective Infrared Irradiation of OH Stretching Modes

In the quest to understand the formation of the building blocks of life, amorphous solid water (ASW) is one of the most widely studied molecular systems. Indeed, ASW is ubiquitous in the cold interstellar medium (ISM), where ASW-coated dust grains provide a catalytic surface for solid phase chemistry, and is believed to be present in the Earth's atmosphere at high altitudes. It has been shown that the ice surface adsorbs small molecules such as CO, N$_2$, or CH$_4$, most likely at OH groups dangling from the surface. Our study presents completely new insights concerning the behaviour of ASW upon selective infrared (IR) irradiation of its dangling modes. When irradiated, these surface H$_2$O molecules reorganise, predominantly forming a stabilised monomer-like water mode on the ice surface. We show that we systematically provoke "hole-burning" effects (or net loss of oscillators) at the wavelength of irradiation and reproduce the same absorbed water monomer on the ASW surface. Our study suggests that all dangling modes share one common channel of vibrational relaxation; the ice remains amorphous but with a reduced range of binding sites, and thus an altered catalytic capacity.

physics.chem-ph↗

arXiv2014

Persistent local order heterogeneity in the supercritical carbon dioxide

The supercritical state is currently viewed as uniform and homogeneous on the pressure-temperature phase diagram in terms of physical properties. Here, we study structural properties of the supercritical carbon dioxide, and discover the existence of persistent medium-range order correlations which make supercritical carbon dioxide non-uniform and heterogeneous on an intermediate length scale, a result not hitherto anticipated. We report on the carbon dioxide heterogeneity shell structure where, in the first shell, both carbon and oxygen atoms experience gas-like type inter- actions with short range order correlations, while within the second shell oxygen atoms essentially exhibit liquid-like type of interactions with medium range order correlations due to localisation of transverse-like phonon packets. We show that the local order heterogeneity remains in the three phase-like equilibrium within very wide temperature range. Importantly, we highlight a catalytic role of atoms inside the nearest neighbor heterogeneity shell in providing a mechanism for diffusion in the supercritical carbon dioxide on an intermediate length scale. Finally, we discuss important implications for answering the intriguing question whether Venus may have had carbon dioxide oceans and urge for an experimental detection of this persistent local order heterogeneity.

cond-mat.stat-mech↗

arXiv2014

Complete quantum state selectivity in cold molecular beams using deflection-resistant dark states in a STIRAP configuration

One of the main goals of chemical dynamics is the creation of molecular beams composed of a single (vibrational, rotational, and magnetic) quantum state of choice. In this paper we show that it is possible to achieve {\it complete} quantum state selectivity by producing resistance to electromagnetically induced deflection (EID) and that the state to be selected can be "dialed in" at will. We illustrate the method by showing in detail how to purify thermal beams of the LiRb and IF molecules to yield molecular beams composed of a variety of pre-chosen single internal quantum states and/or superpositions of such states. We expect that this method will be implemented in all subsequent explorations of the fundamentals of chemical reactions and their control, and the use of cold molecules as a vehicle for studying some of the most profound issues of quantum dynamics.

quant-ph↗

arXiv2014

Electrokinetics of Polar Liquids in Contact with Non-Polar Surfaces

Zeta potentials of several polar protic (water, ethylene glycol, formamide) as well as polar aprotic (dimethyl sulfoxide) liquids were measured in contact with three non-polar surfaces using closed-cell electro-osmosis. The test surfaces were chemisorbed monolayers of alkyl siloxanes, fluoroalkyl siloxanes and polydimethylsiloxanes (PDMS) grafted on glass slides. All these liquids exhibited substantial electrokinetics in contact with the non-polar surfaces with these observations: the electrokinetic effect on the fluorocarbon-coated surface is the strongest; and on a PDMS grafted surface, the effect is the weakest. Even though these hygroscopic liquids contain small amounts of water, the current models of charging based on the adsorption of hydroxide ions at the interface or the dissociation of preexisting functionalities (e.g., silanol groups) appear to be insufficient to account for the various facets of the experimental observations. The results illustrate how ubiquitous the phenomenon of electro-kinetics is with polar liquids contacting such apparently passive non-polar surfaces. We hope that these results will inspire further experimental and theoretical studies in this important area of research that has potential practical implications.

physics.chem-ph↗

arXiv2013

Theory of Nucleation in Phase-separating Nanoparticles

The basic physics of nucleation in solid \hl{single-crystal} nanoparticles is revealed by a phase-field theory that includes surface energy, chemical reactions and coherency strain. In contrast to binary fluids, which form arbitrary contact angles at surfaces, complete "wetting" by one phase is favored at binary solid surfaces. Nucleation occurs when surface wetting becomes unstable, as the chemical energy gain (scaling with area) overcomes the elastic energy penalty (scaling with volume). The nucleation barrier thus decreases with the area-to-volume ratio and vanishes below a critical size, and nanoparticles tend to transform in order of increasing size, leaving the smallest particles homogeneous (in the phase of lowest surface energy). The model is used to simulate phase separation in realistic nanoparticle geometries for \ce{Li_XFePO4}, a popular cathode material for Li-ion batteries, and collapses disparate experimental data for the nucleation barrier, with no adjustable parameters. Beyond energy storage, the theory generally shows how to tailor the elastic and surface properties of a solid nanostructure to achieve desired phase behavior.

cond-mat.mtrl-sci↗

arXiv2013

Mechanically induced metal-insulator transition in carbyne

First-principles calculations for carbyne under strain predict that the Peierls transition from symmetric cumulene to broken-symmetry polyyne structure is enhanced as the material is stretched. Interpretation within a simple and instructive analytical model suggests that this behavior is valid for arbitrary 1D metals. Further, numerical calculations of the anharmonic quantum vibrational structure of carbyne show that zero-point atomic vibrations alone eliminate the Peierls distortion in a mechanically free chain, preserving the cumulene symmetry. The emergence and increase of Peierls dimerization under tension then implies a qualitative transition between the two forms, which our computations place around 3% strain. Thus, zero-point vibrations and mechanical strain jointly produce a change in symmetry resulting in the transition from metallic to insulating state. In any practical realization, it is important that the effect is also chemically modulated by the choice of terminating groups. Our findings are promising for applications such as electromechanical switching and band gap tuning via strain, and besides carbyne itself, they directly extend to numerous other systems that show Peierls distortion.

cond-mat.mtrl-sci↗

arXiv2013

Spectroscopic Properties of Nanotube-Chromophore Hybrids

Recently, individual single-walled carbon nanotubes (SWNTs) functionalized with azo-benzene chromophores were shown to form a new class of hybrid nanomaterials for optoelectronics applications. Here we use a number of experimental techniques and theory to understand the binding, orientation, and nature of coupling between chromophores and the nanotubes, all of which are of relevance to future optimization of these hybrid materials. We find that the binding energy between chromophores and nanotubes depends strongly on the type of tether that is used to bind the chromophores to the nanotubes, with pyrene tethers resulting in more than 90% of the bound chromophores during processing. DFT calculations show that the binding energy of the chromophores to the nanotubes is maximized for chromophores parallel to the nanotube sidewall, even with the use of tethers; second harmonic generation shows that there is nonetheless a partial radial orientation of the chromophores on the nanotubes. We find weak electronic coupling between the chromophores and the SWNTs, consistent with non-covalent binding. The chromophore-nanotube coupling, while weak, is sufficient to quench the chromophore fluorescence. Stern-Volmer plots are non-linear, which supports a combination of static and dynamic quenching processes. The chromophore orientation is an important variable for chromophore-nanotube phototransistors, and our experiments suggest the possibility for further optimizing this orientational degree of freedom.

cond-mat.mes-hall↗

arXiv2013

Carbyne from first principles: Chain of C atoms, a nanorod or a nanorope?

We report an extensive study of the properties of carbyne using first-principles calculations. We investigate carbyne's mechanical response to tension, bending, and torsion deformations. Under tension, carbyne is about twice as stiff as the stiffest known materials and has an unrivaled specific strength of up to 7.5*10^7 Nm/kg, requiring a force of ~10 nN to break a single atomic chain. Carbyne has a fairly large room-temperature persistence length of about 14 nm. Surprisingly, the torsional stiffness of carbyne can be zero but can be 'switched on' by appropriate functional groups at the ends. Further, under appropriate termination, carbyne can be switched into a magnetic-semiconductor state by mechanical twisting. We reconstruct the equivalent continuum-elasticity representation, providing the full set of elastic moduli for carbyne, showing its extreme mechanical performance (e.g. a nominal Young's modulus of 32.7 TPa with an effective mechanical thickness of 0.772 A). We also find an interesting coupling between strain and band gap of carbyne, which is strongly increased under tension, from 3.2 to 4.4 eV under a 10% strain. Finally, we study the performance of carbyne as a nanoscale electrical cable, and estimate its chemical stability against self-aggregation, finding an activation barrier of 0.6 eV for the carbyne-carbyne cross-linking reaction and an equilibrium cross-link density for two parallel carbyne chains of 1 cross-link per 17 C atoms (2.2 nm).

cond-mat.mtrl-sci↗

arXiv2014

Entropically Patchy Particles: Engineering Valence through Shape Entropy

Patchy particles are a popular paradigm for the design and synthesis of nanoparticles and colloids for self-assembly. In "traditional" patchy particles, anisotropic interactions arising from patterned coatings, functionalized molecules, DNA, and other enthalpic means create the possibility for directional binding of particles into higher-ordered structures. Although the anisotropic geometry of non-spherical particles contributes to the interaction patchiness through van der Waals, electrostatic, and other interactions, how particle shape contributes entropically to self-assembly is only now beginning to be understood. It has been recently demonstrated that, for hard shapes, entropic forces are directional. A newly proposed theoretical framework that defines and quantifies directional entropic forces demonstrates the anisotropic--that is, patchy--nature of these emergent, attractive forces. Here we introduce the notion of entropically patchy particles as the entropic counterpart to enthalpically patchy particles. Using three example "families" of shapes, we judiciously modify entropic patchiness by introducing geometric features to the particles so as to target specific crystal structures, which then assembled with Monte Carlo simulations. We quantify the emergent entropic valence via a potential of mean force and torque. We generalize these shape operations to shape anisotropy dimensions, in analogy with the anisotropy dimensions introduced for enthalpically patchy particles. Our findings demonstrate that entropic patchiness and emergent valence provide a way of engineering directional bonding into nanoparticle systems, whether in the presence or absence of additional, non-entropic forces.

cond-mat.soft↗

arXiv2011

Non-thermal escape of molecular hydrogen from Mars

We present a detailed theoretical analysis of a non-thermal escape of molecular hydrogen from Mars induced by collisions with hot atomic oxygen from martian corona. To accurately describe the energy transfer in O + H$_2(v,j)$ collisions, we performed extensive quantum-mechanical calculations of state-to-state elastic, inelastic, and reactive cross sections. The escape flux of H$_2$ molecules was evaluated using a simplified 1D column model of the martian atmosphere with realistic densities of atmospheric gases and hot oxygen production rates for the low solar activity conditions. An average density of the non-thermal escape flux of H$_2$ of $1.9\times10^5$ cm$^{-2}$s$^{-1}$ was obtained considering energetic O atoms produced in dissociative recombinations of O$_{2}^{+}$ ions. Predicted rovibrational distribution of the escaping H$_2$ was found to contain a significant fraction of higher rotational states. While the non-thermal escape rate was found to be lower than Jeans flux for H$_2$ molecules, the non-thermal escape rates of HD and D$_2$ are significantly higher than their respective Jeans rates. The accurate values of non-thermal escape fluxes of different molecular isotopes of H$_2$ may be important in analyses of evolution of the martian atmosphere. The described molecular ejection mechanism is general and expected to contribute to atmospheric escape of H$_2$ and other light molecules from planets, satellites, and exoplanetary bodies.

astro-ph.EP↗