Slow magnetic relaxation in a heteroleptic anilate-based DyIII metal-organic framework.

Novel heteroleptic anilate-based lanthanide MOFs (LnIII = Tb, Dy, Ho) have been obtained under hydrothermal conditions by the ancillary ligand synthetic strategy. These structurally isomorphous species contain octacoordinated LnIII ions with coordination polyhedra approaching an ideal D2d symmetry, best described by a distorted biaugmented trigonal prismatic C2v geometry. In the whole series, only the Dy-MOF exhibits SMM behaviour.

Strong Anharmonicity at the Origin of Anomalous Thermal Conductivity in Double Perovskite Cs2 NaYbCl6.

Anomalous thermal transport of Cs2 NaYbCl6 double-halide perovskite above room temperature is reported and rationalized. Calculations of phonon dispersion relations and scattering rates up to the fourth order in lattice anharmonicity have been conducted to determine their effective dependence on temperature. These findings show that specific phonon group velocities and lifetimes increase if the temperature is raised above 500 K. This, in combination with anharmonicity, provides the microscopic mechanism responsible for the increase in lattice thermal conductivity at high temperatures, contrary to the predictions of phonon transport theories based on solely cubic anharmonicity. The model accurately and quantitatively reproduces the experimental thermal conductivity data as a function of temperature.

Thermally Promoted Cation Exchange at the Solid State in the Transmission Electron Microscope: How It Actually Works.

Cation exchange offers a strong postsynthetic tool for nanoparticles that are unachievable via direct synthesis, but its velocity makes observing the onset of the reaction in the liquid state almost impossible. After successfully proving that cation exchange reactions can be triggered, performed, and followed live at the solid state by an in situ transmission electron microscopy approach, we studied the deep mechanisms ruling the onset of cation exchange reactions, i.e., the adsorption, penetration, and diffusion of cations in the host matrices of two crystal phases of CdSe. Exploiting an in situ scanning transmission electron microscopy approach with a latest generation heating holder, we were able to trigger, freeze, and image the initial stages of cation exchange with much higher detail. Also, we found a connection between the crystal structure of CdSe, the starting temperature, and the route of the cation exchange reaction. All the experimental results were further reviewed by molecular dynamics simulations of the whole cation exchange reaction divided in subsequent steps. The simulations highlighted how the cation exchange mechanism and the activation energies change with the host crystal structures. Furthermore, the simulative results strongly corroborated the activation temperatures and the cation exchange rates obtained experimentally, providing a deeper understanding of its phenomenology and mechanism at the atomic scale.

Roadmap on thermoelectricity.

The increasing energy demand and the ever more pressing need for clean technologies of energy conversion pose one of the most urgent and complicated issues of our age. Thermoelectricity, namely the direct conversion of waste heat into electricity, is a promising technique based on a long-standing physical phenomenon, which still has not fully developed its potential, mainly due to the low efficiency of the process. In order to improve the thermoelectric performance, a huge effort is being made by physicists, materials scientists and engineers, with the primary aims of better understanding the fundamental issues ruling the improvement of the thermoelectric figure of merit, and finally building the most efficient thermoelectric devices. In this Roadmap an overview is given about the most recent experimental and computational results obtained within the Italian research community on the optimization of composition and morphology of some thermoelectric materials, as well as on the design of thermoelectric and hybrid thermoelectric/photovoltaic devices.

Carbon Nanodots from an In Silico Perspective.

Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.

The interplay of chemical structure, physical properties, and structural design as a tool to modulate the properties of melanins within mesopores.

The design of modern devices that can fulfil the requirements for sustainability and renewable energy applications calls for both new materials and a better understanding of the mixing of existing materials. Among those, surely organic-inorganic hybrids are gaining increasing attention due to the wide possibility to tailor their properties by accurate structural design and materials choice. In this work, we'll describe the tight interplay between porous Si and two melanic polymers permeating the pores. Melanins are a class of biopolymers, known to cause pigmentation in many living species, that shows very interesting potential applications in a wide variety of fields. Given the complexity of the polymerization process beyond the formation and structure, the full understanding of the melanins' properties remains a challenging task. In this study, the use of a melanin/porous Si hybrid as a tool to characterize the polymer's properties within mesopores gives new insights into the conduction mechanisms of melanins. We demonstrate the dramatic effect induced on these mechanisms in a confined environment by the presence of a thick interface. In previous studies, we already showed that the interactions at the interface between porous Si and eumelanin play a key role in determining the final properties of composite materials. Here, thanks to a careful monitoring of the photoconductivity properties of porous Si filled with melanins obtained by ammonia-induced solid-state polymerization (AISSP) of 5,6-dihydroxyindole (DHI) or 1,8-dihydroxynaphthalene (DHN), we investigate the effect of wet, dry, and vacuum cycles of storage from the freshly prepared samples to months-old samples. A computational study on the mobility of water molecules within a melanin polymer is also presented to complete the understanding of the experimental data. Our results demonstrate that: (a) the hydration-dependent behavior of melanins is recovered in large pores (≈ 60 nm diameter) while is almost absent in thinner pores (≈ 20 nm diameter); (b) DHN-melanin materials can generate higher photocurrents and proved to be stable for several weeks and more sensitive to the wet/dry variations.

Thermal conduction and rectification phenomena in nanoporous silicon membranes.

Non-equilibrium molecular dynamics simulations have been applied to study thermal transport properties, such as thermal conductivity and rectification, in nanoporous Si membranes. Cylindrical pores have been generated in crystalline Si membranes with different configurations, including step-like, ordered and random pore distributions. The effect of interface and overall porosity on thermal transport properties has been investigated as well as the impact of the porosity profile on the direction of the heat current. The lowest thermal conductivity and highest thermal rectification for equal porosity have been found for a step-like pore distribution. Increasing interface porosity resulted in an increase of thermal rectification, which has been found to be systematically higher for random pore distribution with respect to an ordered one. Furthermore, a maximum in rectification of 5.5% has been found for a specific overall porosity (Φtot = 0.02) in samples with constant interface porosity and ordered pore distribution. This has been attributed to an increased effect of asymmetric interface boundary resistance resulting from increased fluctuations of the latter with altering temperature. The average value of the interface boundary resistance has been found to decrease with increasing porosity for samples with ordered pore distribution leading to a decrease in thermal rectification.

Strong Suppression of Thermal Conductivity in the Presence of Long Terminal Alkyl Chains in Low-Disorder Molecular Semiconductors.

While the charge transport properties of organic semiconductors have been extensively studied over the recent years, the field of organics-based thermoelectrics is still limited by a lack of experimental data on thermal transport and of understanding of the associated structure-property relationships. To fill this gap, a comprehensive experimental and theoretical investigation of the lattice thermal conductivity in polycrystalline thin films of dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene (Cn-DNTT-Cn with n = 0, 8) semiconductors is reported. Strikingly, thermal conductivity appears to be much more isotropic than charge transport, which is confined to the 2D molecular layers. A direct comparison between experimental measurements (3ω-Völklein method) and theoretical estimations (approach-to-equilibrium molecular dynamics (AEMD) method) indicates that the in-plane thermal conductivity is strongly reduced in the presence of the long terminal alkyl chains. This evolution can be rationalized by the strong localization of the intermolecular vibrational modes in C8-DNTT-C8 in comparison to unsubstituted DNTT cores, as evidenced by a vibrational mode analysis. Combined with the enhanced charge transport properties of alkylated DNTT systems, this opens the possibility to decouple electron and phonon transport in these materials, which provides great potential for enhancing the thermoelectric figure of merit ZT.

Observation of second sound in a rapidly varying temperature field in Ge.

Second sound is known as the thermal transport regime where heat is carried by temperature waves. Its experimental observation was previously restricted to a small number of materials, usually in rather narrow temperature windows. We show that it is possible to overcome these limitations by driving the system with a rapidly varying temperature field. High-frequency second sound is demonstrated in bulk natural Ge between 7 K and room temperature by studying the phase lag of the thermal response under a harmonic high-frequency external thermal excitation and addressing the relaxation time and the propagation velocity of the heat waves. These results provide a route to investigate the potential of wave-like heat transport in almost any material, opening opportunities to control heat through its oscillatory nature.

Room temperature second sound in cumulene.

Second sound is known as the thermal transport regime occurring in a wave-like fashion, usually identified in a limited number of materials only at cryogenic temperatures. Here we show that second sound in a µm-long carbon chain (cumulene) might occur even at room temperature. To this aim, we calibrate a many-body force field on the first principles calculated phonon dispersion relations of cumulene and, through molecular dynamics, we mimic laser-induced transient thermal grating experiments. We provide evidence that by tuning temperature as well as the space modulation of its initial profile we can reversibly drive the system from a wave-like to a diffusive-like thermal transport. By following three different theoretical methodologies (molecular dynamics, the Maxwell-Cattaneo-Vernotte equation, and heat transport microscopic theory) we estimate for cumulene a second sound velocity in the range of 2.4-3.2 km s-1.

Thermal conductivity of benzothieno-benzothiophene derivatives at the nanoscale.

We study by scanning thermal microscopy the nanoscale thermal conductance of films (40-400 nm thick) of [1]benzothieno[3,2-b][1]benzothiophene (BTBT) and 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT-C8). We demonstrate that the out-of-plane thermal conductivity is significant along the interlayer direction, larger for BTBT (0.63 ± 0.12 W m-1 K-1) compared to C8-BTBT-C8 (0.25 ± 0.13 W m-1 K-1). These results are supported by molecular dynamics calculations (approach to equilibrium molecular dynamics method) performed on the corresponding molecular crystals. The calculations point to significant thermal conductivity (3D-like) values along the 3 crystalline directions, with anisotropy factors between the crystalline directions below 1.8 for BTBT and below 2.8 for C8-BTBT-C8, in deep contrast with the charge transport properties featuring a two-dimensional character for these materials. In agreement with the experiments, the calculations yield larger values in BTBT compared to C8-BTBT-C8 (0.6-1.3 W m-1 K-1versus 0.3-0.7 W m-1 K-1, respectively). The weak thickness dependence of the nanoscale thermal resistance is in agreement with a simple analytical model.

Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution.

Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.

Deciphering Molecular Mechanisms of Interface Buildup and Stability in Porous Si/Eumelanin Hybrids.

Porous Si/eumelanin hybrids are a novel class of organic-inorganic hybrid materials that hold considerable promise for photovoltaic applications. Current progress toward device setup is, however, hindered by photocurrent stability issues, which require a detailed understanding of the mechanisms underlying the buildup and consolidation of the eumelanin-silicon interface. Herein we report an integrated experimental and computational study aimed at probing interface stability via surface modification and eumelanin manipulation, and at modeling the organic-inorganic interface via formation of a 5,6-dihydroxyindole (DHI) tetramer and its adhesion to silicon. The results indicated that mild silicon oxidation increases photocurrent stability via enhancement of the DHI-surface interaction, and that higher oxidation states in DHI oligomers create more favorable conditions for the efficient adhesion of growing eumelanin.

Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

Tuning the thermal conductivity of methylammonium lead halide by the molecular substructure.

By using state-of-the-art atomistic methods we provide an accurate estimate of thermal conductivity of methylammonium lead halide as a function of sample size and temperature, in agreement with experimental works. We show that the thermal conductivity of methylammonium lead halide is intrinsically low, due to the low sound velocity of the PbI lattice. Furthermore, by selectively analyzing the effect of different molecular degrees of freedom, we clarify the role of the molecular substructure by showing that the internal modes above 150 cm(-1) (in addition to rotations) are effective in reducing the thermal conductivity of hybrid perovskites. This analysis suggests strategies to tailor the thermal conductivity by modifying the internal structure of organic cations.

Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations.

Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand-protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed.

Lattice thermal conductivity of Si(1-x)Ge(x) nanocomposites.

We calculate the lattice thermal conductivity in model Si(1-x)Ge(x) nanocomposites by molecular dynamics in a transient thermal conduction regime. Our simulations provide evidence that thermal transport depends only marginally on stoichiometry in the range 0.2≤x≤0.8, while it is deeply affected by the granulometry. In particular, we show that Si(1-x)Ge(x) nanocomposites have lattice thermal conductivity below the corresponding bulk alloy with the same stoichiometry. The main role in affecting thermal conduction is provided by grain boundaries, which largely affect vibrational modes with a long mean-free path.

Self-assembling of zinc phthalocyanines on ZnO (1010) surface through multiple time scales.

We adopt a hierarchic combination of theoretical methods to study the assembling of zinc phthalocyanines (ZnPcs) on a ZnO (1010) surface through multiple time scales. Atomistic simulations, such as model potential molecular dynamics and metadynamics, are used to study the energetics and short time evolution (up to ∼100 ns) of small ZnPc aggregates. The stability and the lifetime of large clusters is then studied by means of an atomistically informed coarse-grained model using classical molecular dynamics. Finally, the macroscopic time scale clustering phenomenon is studied by Metropolis Monte Carlo algorithms as a function of temperature and surface coverage. We provide evidence that at room temperature the aggregation is likely to occur at sufficiently high coverage, and we characterize the nature, morphology, and lifetime of ZnPc's clusters. We identify the molecular stripes oriented along [010] crystallographic directions as the most energetically stable aggregates.

Rapid desensitization of the rat α7 nAChR is facilitated by the presence of a proline residue in the outer ß-sheet.

The rat α7 nicotinic acetylcholine receptor (nAChR) has a proline residue near the middle of the ß9 strand. The replacement of this proline residue at position 180 (P180) by either threonine (α7-P180T) or serine (α7-P180S) slowed the onset of desensitization dramatically, with half-times of ~930 and 700 ms, respectively, compared to 90 ms for the wild-type receptor. To investigate the importance of the hydroxyl group on the position 180 side-chains, the mutant receptors α7-P180Y and α7-P180F were studied and showed half-times of desensitization of 650 and 160 ms, respectively. While a position 180 side-chain OH group may contribute to the slow desensitization rates, α7-P180S and α7-P180V resulted in receptors with similar desensitization rates, suggesting that increased backbone to backbone H bonding expected in the absence of proline at position 180 would likely exert a great effect on desensitization. Single channel recordings indicated that for the α7-P180T receptor there was a significantly reduced closed time without any change in single channel conductance (as compared to wild-type). Kinetic simulations indicated that all changes observed for the mutant channel behaviour were reproduced by decreasing the rate of desensitization, and increasing the microscopic affinity to resting receptors. Molecular dynamics (MD) simulations on a homology model were used to provide insight into likely H bond interactions within the outer ß-sheet that occur when the P180 residue is mutated. All mutations analysed increased about twofold the predicted number of H bonds between the residue at position 180 and the backbone of the ß10 strand. Moreover, the α7-P180T and α7-P180S mutations also formed some intrastrand H bonds along the ß9 strand, although H bonding of the OH groups of the threonine or serine side-chains was predicted to be infrequent. Our results indicate that rapid desensitization of the wild-type rat α7 nAChR is facilitated by the presence of the proline residue within the ß9 strand.

Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor.

Trans-cis isomerization of a proline peptide bond is a potential mechanism to open the channel of the 5-HT(3) receptor. Here, we have used the metadynamics method to theoretically explore such a mechanism. We have determined the free energy surfaces in aqueous solution of a series of dipeptides of proline analogues and evaluated the free energy difference between the cis and trans isomers. These theoretical results were then compared with data from mutagenesis experiments, in which the response of the 5-HT(3) receptor was measured when the proline at the apex of the M2-M3 transmembrane domain loop was mutated. The strong correlation between the experimental and the theoretical data supports the existence of a trans-cis proline switch for opening the 5-HT(3) receptor ion channel.