Assessing the thermal conductivity of amorphous SiN by approach-to-equilibrium molecular dynamics.

First-principles molecular dynamics combined with the approach-to-equilibrium molecular dynamics methodology is employed to calculate the thermal conductivity of non-stoichiometric amorphous SiN. This is achieved by implementing thermal transients in five distinct models of different sizes along the direction of the heat transport. Such models have identical structural features and are representative of the same material, thereby allowing for a reliable analysis of thermal conductivity trends as a function of the relevant cell dimension. In line with the known physical law of heat propagation at short scale, the thermal conductivity increases in size with the direction of heat transport. The observed behavior is rationalized accounting for previous results on crystalline and amorphous materials, thus providing a unified description holding for a large class of materials and spanning a wide range of heat propagation lengths.

Exciton diffusion in poly(3-hexylthiophene) by first-principles molecular dynamics.

Poly(3-hexylthiophene) (P3HT) is a polymer used in organic solar cells as a light absorber and an electron donor. Photogenerated excitons diffuse and dissociate into free charge carriers provided they reach the absorber boundaries. The device efficiency is therefore dependent on the exciton diffusion. Although measurements can be performed for example by time-resolved photoluminescence, a quantitative modeling is highly desirable to get an insight into the relationship between the atomic structure at finite temperature and the diffusion coefficient of the exciton. This is the objective of the present work, achieved by resorting to first-principles molecular dynamics in combination with the restricted open-shell approach to model the singlet excited state. The maximally localized Wannier functions and their centers are used to monitor and localize the electron and the hole along the dynamics. The resulting diffusion coefficient is in close agreement with available measurements.

Enantioselective amino acid interactions in solution.

Enantiomeric excesses (ee) of L-amino acids in meteorites are higher than 10%, especially for isovaline (Iva). This suggests the existence of some kind of triggering mechanism responsible for the amplification of the ee from an initial small value. Here, we investigate the dimeric molecular interactions of alanine (Ala) and Iva in solution as an initial nucleation step of crystals at an accurate first-principles level. We find that the dimeric interaction of Iva is more chirality-dependent than that of Ala, thus providing a clear molecular-level insight into the enantioselectivity of amino acids in solution.

Impact of the local atomic structure on the thermal conductivity of amorphous Ge2Sb2Te5.

Thermal properties are expected to be sensitive to the network topology, and however, no clearcut information is available on how the thermal conductivity of amorphous systems is affected by details of the atomic structure. To address this issue, we use as a target system a phase-change amorphous material (i.e., Ge2Sb2Te5) simulated by first-principles molecular dynamics combined with the approach-to-equilibrium molecular dynamics technique to access the thermal conductivity. Within the density-functional theory, we employed two models sharing the same exchange-correlation functional but differing in the pseudopotential (PP) implementation [namely, Trouiller-Martins (TM) and Goedecker, Teter, and Hutter (GTH)]. They are both compatible with experimental data, and however, the TM PP construction results in a Ge tetrahedral environment largely predominant over the octahedral one, although the proportion of tetrahedra is considerably smaller when the GTH PP is used. We show that the difference in the local structure between TM and GTH models impacts the vibrational density of states while the thermal conductivity does not feature any appreciable sensitivity to such details. This behavior is rationalized in terms of extended vibrational modes.

Organocatalytic-racemization reaction elucidation of aspartic acid by density functional theory.

Aldehydes and carboxylic acids are widely used as catalysts for efficient racemization process of amino acids. However, the detailed reaction mechanism remains unclear. This work aims to clarify the racemization mechanism of aspartic acid (Asp) catalyzed by salicylaldehyde and acetic acid by using computational approaches. Density functional theory was used to obtain the structures and relative energies of 10 intermediates and five transition states, thus characterizing the main stages of the reaction. The calculated energy diagram shows that the dehydration step has the highest energy barrier, followed by the reaction step to change the chirality of Asp, which is a crucial process for racemization. In the dehydration reaction, water molecules can induce a remarkable decrease in the required energy.

Structural, dynamical, and electronic properties of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide.

We provide a microscopic insight, both structural and electronic, into the multifold interactions occurring in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [EMIM][TFSI] currently targeted for applications in next-generation low-power electronics and optoelectronic devices. To date, practical applications have remained hampered by the lack of fundamental understanding of the interactions occurring both inside the IL and at the interface with the substrate. Our first principles dynamical simulations provide accurate insights into the nature of bonding and non-bonding interactions, dynamical conformational changes and induced dipole moments, along with their statistical distributions, of this ionic liquid, that have so far not been completely unraveled. The mobilities of the two ionic species are obtained by long-lasting dynamical simulations at finite temperature, allowing simultaneous monitoring and quantification of the isomerization occurring in the IL. Moreover, a thorough analysis of the electronic structure and partial charge distributions characterizing the two components, the cation and anion, allow rationalization of the nature of the electrostatic interactions, hydrogen bonding properties of the two ionic counterparts, and the infra-red and dielectric response of the system, especially in the low frequency range, for the full characterization of the IL.

Impact of Dispersion Force Schemes on Liquid Systems: Comparing Efficiency and Drawbacks for Well-Targeted Test Cases.

First-principles molecular dynamics (FPMD) calculations were performed on liquid GeSe4 with the aim of inferring the impact of dispersion (van der Waals, vdW) forces on the structural properties. Different expressions for the dispersion forces were employed, allowing us to draw conclusions on their performances in a comparative fashion. These results supersede previous FPMD calculations obtained in smaller systems and shorter time trajectories by providing data of unprecedented accuracy. We obtained a substantial agreement with experiments for the structure factor regardless of the vdW scheme employed. This objective was achieved by using (in addition to FPMD with no dispersion forces) a selection of vdW schemes available within density functional theory. The first two are due to Grimme, D2 and D3, and the third one is devised within the so-called maximally localized Wannier functions approach (MLWF). D3 results feature a sizeable disagreement in real space with D2 and MLWF in terms of the partial and total pair correlation functions as well as the coordination numbers. More strikingly, total and partial structure factors calculated with D3 exhibit an unexpected sharp increase at low k. This peculiarity goes along with large void regions within the network, standing for a phase separation of indecipherable physical meaning. In view of these findings, further evidence of unconventional structural properties found by employing D3 is presented by relying on results obtained for a complex ionic liquid supported on a solid surface. The novelty of our study is multifold: new, reliable FPMD data for a prototypical disordered network system, convincing agreement with experimental data and assessment of the impact of dispersion forces, with emphasis on the intriguing behavior of one specific recipe and the discovery of common structural features shared by drastically dissimilar physical systems when the D3 vdW scheme is employed.

Reaction mechanism of N-cyclopropylglycine oxidation by monomeric sarcosine oxidase.

Monomeric sarcosine oxidase (MSOX) is a fundamental - yet one of the simplest - member of a family of flavoenzymes able to catalyze the oxidation of sarcosine (N-methylglycine) and other secondary amines. MSOX is one of the best characterized members of the amine oxidoreductases (AOs), however, its reaction mechanism is still controversial. A single electron transfer (SET) process was suggested on the basis of studies with N-cyclopropylglycine (CPG), although a hydride transfer mechanism would be more consistent in general for AOs. To shed some light on the detailed reaction mechanisms of CPG in MSOX, we performed hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. We found that the polar mechanism is energetically the most favorable. The free energy profile indicates that the first rate-limiting step is the CPG binding to the flavin ring which simultaneously proceeds with the ring-opening of the CPG cyclopropyl group. This reaction step of the CPG adduct formation corresponds to the nucleophilic attack of the cyclopropyl group (C3 atom) to the flavin ring (C4a atom), whereas the expected radical species formation in the SET mechanism was not observed. The following inactivated species, which accumulates during the CPG oxidation in MSOX, can be ascribed to an imine state, and not an enamine state, on the basis of the computed UV/Vis spectra. The conformation of CPG was found to be crucial for reactions following the CPG adduct formation.

Thermal resistance of an interfacial molecular layer by first-principles molecular dynamics.

The approach-to-equilibrium molecular dynamics (AEMD) methodology is applied in combination with first-principles molecular dynamics to investigate the thermal transfer between two silicon blocks connected by a molecular layer. Our configuration consists of alkanes molecules strongly coupled to the silicon surfaces via covalent bonds. In phase 1 of AEMD, the two Si blocks are thermalized at high and low temperatures to form the hot and cold reservoirs. During phase 2 of AEMD, a transfer between reservoirs occurs until thermal equilibrium is reached. The transfer across the interface dominates the transient over heat conduction within the reservoirs. The value of the thermal interface conductance is in agreement with the experimental data obtained for analogous bonding cases between molecules and reservoirs. The dependence on the length of the thermal interface resistance features two contributions. One is constant (the resistance at the silicon/molecule interface), while the other varies linearly with the length of the molecular chains (diffusive transport). The corresponding value of the thermal conductivity agrees well with experiments.

Hydrogen storage mechanism and diffusion in metal-organic frameworks.

Diffusion and storage of hydrogen molecules in metal-organic frameworks are crucial for the development of next-generation energy storage devices. By resorting to the first principles modeling, we compute the diffusion coefficient of molecular hydrogen in these systems in a range of temperatures where MOF-based devices are expected to operate. The explicit inclusion of the electronic structure shows that diffusivities are one order of magnitude smaller than those reported by classical simulations, evidencing the insufficiency of the empirical force fields used so far. We show that hydrogen is mainly rolled up around the metal oxide nodes both in MOF-5 and IRMOF-6, and partly around the carbon atoms in the case of IRMOF-6, where charged linkers are present. Metal ions embedded in the junction sites exert an electrostatic attraction toward hydrogen and the resulting distribution shows some ordering around these same sites at low temperature, whereas this tendency vanishes at room temperature. The induced polarization of hydrogen molecules generates an electrostatic interaction with charged atoms inside these nano-scaffolds and this is a key factor for the enhancement in hydrogen storage both in MOF-5 and IRMOF-6. The mechanism discussed hereby provides a novel understanding of metal-organic frameworks and acts as a guide to tune their efficiency for hydrogen storage. Moreover it paves the way to a computer-aided design of effective MOFs indicating that a fine control of the distribution of electrostatic charges inside the hydrogen hosting structure is crucial.

Synthesis and Characterization of Non-Isolated-Pentagon-Rule Actinide Endohedral Metallofullerenes U@ C1(17418)-C76, U@ C1(28324)-C80, and Th@ C1(28324)-C80: Low-Symmetry Cage Selection Directed by a Tetravalent Ion.

For the first time, actinide endohedral metallofullerenes (EMFs) with non-isolated-pentagon-rule (non-IPR) carbon cages, U@C80, Th@C80, and U@C76, have been successfully synthesized and fully characterized by mass spectrometry, single crystal X-ray diffractometry, UV-vis-NIR and Raman spectroscopy, and cyclic voltammetry. Crystallographic analysis revealed that the U@C80 and Th@C80 share the same non-IPR cage of C1(28324)-C80, and U@C76 was assigned to non-IPR U@ C1(17418)-C76. All of these cages are chiral and have never been reported before. Further structural analyses show that enantiomers of C1(17418)-C76 and C1(28324)-C80 share a significant continuous portion of the cage and are topologically connected by only two C2 insertions. DFT calculations show that the stabilization of these unique non-IPR fullerenes originates from a four-electron transfer, a significant degree of covalency, and the resulting strong host-guest interactions between the actinide ions and the fullerene cages. Moreover, because the actinide ion displays high mobility within the fullerene, both the symmetry of the carbon cage and the possibility of forming chiral fullerenes play important roles to determine the isomer abundances at temperatures of fullerene formation. This study provides what is probably one of the most complete examples in which carbon cage selection occurs through thermodynamic control at high temperatures, so the selected cages do not necessarily coincide with the most stable ones at room temperature. This work also demonstrated that the metal-cage interactions in actinide EMFs show remarkable differences from those previously known for lanthanide EMFs. These unique interactions not only could stabilize new carbon cage structures, but more importantly, they lead to a new family of metallofullerenes for which the cage selection pattern is different to that observed so far for nonactinide EMFs. For this new family, the simple ionic A q+@C2 n q- model makes predictions less reliable, and in general, unambiguously discerning the isolated structures requires the combination of accurate computational and experimental data.

A detailed insight into the catalytic reduction of NO operated by Cr-Cu nanostructures embedded in a CeO2 surface.

Replacing rare and expensive elements, such as Pt, Pd, and Rh, commonly used in catalytic devices with more abundant and less expensive ones is mandatory to realize efficient, sustainable and economically appealing three-way catalysts. In this context, the surface of a Cr-Cu/CeO2 system represents a versatile catalyst for the conversion of toxic NO into harmless N2. Yet, a clear picture of the underlying mechanism is still missing. We provide here a detailed insight into such a reaction mechanism by means of a combined experimental and theoretical study. Fourier-transform infrared spectroscopy is used to detect all the products resulting from catalytic reactions of NO and CO on the surface of a Cr-Cu/CeO2 nanocatalyst. CO pulsing experiments unveil that reactions of CO with O atoms at the Cr-Cu/CeO2 surface are the major factors responsible for the formation of surface vacancies. On these grounds, a comprehensive picture of the NO reduction and the role of both Cu and Cr dopants and vacancies is rationalized by first-principles modeling. Our findings provide a general route for the realization of ceria-based cost-effective catalysts.

Simple but Efficient Method for Inhibiting Sintering and Aggregation of Catalytic Pt Nanoclusters on Metal-Oxide Supports.

A simple and efficient method to inhibit aggregation of Pt clusters supported on metal oxide was developed, preserving the accessible clusters surface where catalytically active sites are located even at relatively high temperatures up to 700 K. The key idea was the inclusion of transition metal atoms such as Ni into the Pt clusters, thus anchoring the clusters through formation of strong chemical bonds with oxygen atoms of the metal-oxide support. To elucidate the efficiency of the method, first-principles molecular dynamics enhanced with free-energy sampling methods were used. These virtual experiments showed how doped Ni atoms, having a stronger affinity to O than Pt, anchor the Pt clusters tightly to the metal-oxide supports and inhibit their tendency to aggregate on the support.

An atomic-level insight into the basic mechanism responsible for the enhancement of the catalytic oxidation of carbon monoxide on a Cu/CeO2 surface.

The reaction mechanisms of CO molecules interacting with a Cu/CeO2 surface and related morphological modifications occurring upon removal of O atoms to generate CO2 are investigated by first-principles dynamical simulations complemented by a free-energy sampling technique. We show that the reactivity of oxygen atoms located in the first layer in the vicinity of the Cu site is remarkably high because of a reduction of the O coordination number. Moreover, we evidence that the doped Cu atoms are responsible for an enhancement of the exposure of other surrounding O atoms, even below the first surface layer, which can then easily react with CO and are gradually removed from the system in the oxidation process. The underlying mechanism responsible for such a high catalytic reactivity of the Cu/CeO2 surface toward CO oxidation is rationalized in terms of the characteristics of the doped Cu. In fact, this copper site is responsible for providing an increasing number of O atoms participating in the catalysis by exposing subsequently all O atoms in the vicinity which are likely to react with an approaching CO. This peculiarity of the Cu atoms extends to O atoms which initially can be deeply buried up to the fourth layer underneath the surface. The mechanism unveiled here provides useful insights into the fundamental mechanism and suggests strategies for the engineering and design of more effective ceria-based catalysts via metal doping.

How seaweeds release the excess energy from sunlight to surrounding sea water.

We report an atomistic insight into the mechanism regulating the energy released by a porphyra-334 molecule, the ubiquitous photosensitive component of marine algae, in a liquid water environment upon an electron excitation. To quantify this rapidly occurring process, we resort to the Fourier analysis of the mass-weighted auto-correlation function, providing evidence for a remarkable dynamic change in the number of hydrogen bonds among water molecules and between the porphyra-334 and its surrounding hydrating water. Hydrogen bonds between the porphyra-334 and close by water molecules can act directly and rather easily to promote an efficient transfer of the excess kinetic energies of the porphyra-334 to the surrounding solvating water molecules via an activation of the collective modes identified as hydrogen-bond stretching modes in liquid water which eventually results in a disruption of the hydrogen bond network. Since porphyra-334 is present in seaweeds, aquatic cyanobacteria (blue-green algae) and red algae, our findings allow addressing the question how algae in oceans or lakes, upon sunlight absorption, can release large amounts of energy into surrounding water without destabilizing neither their own nor the H2O molecular structure.

Thermal conductivity of glassy GeTe4 by first-principles molecular dynamics.

A transient thermal regime is achieved in glassy GeTe4 by first-principles molecular dynamics following the recently proposed "approach-to-equilibrium" methodology. The temporal and spatial evolution of the temperature do comply with the time-dependent solution of the heat equation. We demonstrate that the time scales required to create the hot and the cold parts of the system and observe the resulting approach to equilibrium are accessible to first-principles molecular dynamics. Such a strategy provides the thermal conductivity from the characteristic decay time. We rationalize in detail the impact on the thermal conductivity of the initial temperature difference, the equilibration duration, and the main simulation features.

Impact of dispersion forces on the atomic structure of a prototypical network-forming disordered system: The case of liquid GeSe2.

A set of structural properties of liquid GeSe2 are calculated by using first-principles molecular dynamics and including, for the first time, van der Waals dispersion forces. None of the numerous atomic-scale simulations performed in the past on this prototypical disordered network-forming material had ever accounted for dispersion forces in the expression of the total energy. For this purpose, we employed either the Grimme-D2 or the maximally localized Wannier function scheme. We assessed the impact of dispersion forces on properties such as partial structure factors, pair correlation functions, bond angle distribution, and number of corner vs edge sharing connections. The maximally localized Wannier function scheme is more reliable than the Grimme-D2 scheme in reproducing existing first-principles results. In particular, the Grimme-D2 scheme worsens the agreement with experiments in the case of the Ge-Ge pair correlation function. Our study shows that the impact of dispersion forces on disordered chalcogenides has to be considered with great care since it cannot be necessarily the same when adopting different recipes.

Reducing the Cost and Preserving the Reactivity in Noble-Metal-Based Catalysts: Oxidation of CO by Pt and Al-Pt Alloy Clusters Supported on Graphene.

The oxidation mechanisms of CO to CO2 on graphene-supported Pt and Pt-Al alloy clusters are elucidated by reactive dynamical simulations. The general mechanism evidenced is a Langmuir-Hinshelwood (LH) pathway in which O2 is adsorbed on the cluster prior to the CO oxidation. The adsorbed O2 dissociates into two atomic oxygen atoms thus promoting the CO oxidation. Auxiliary simulations on alloy clusters in which other metals (Al, Co, Cr, Cu, Fe, Ni) replace a Pt atom have pointed to the aluminum doped cluster as a special case. In the nanoalloy, the reaction mechanism for CO oxidation is still a LH pathway with an activation barrier sufficiently low to be overcome at room temperature, thus preserving the catalyst efficiency. This provides a generalizable strategy for the design of efficient, yet sustainable, Pt-based catalysts at reduced cost.

The absence of a gap state and enhancement of the Mars-van Krevelen reaction on oxygen defective Cu/CeO2 surfaces.

We report a detailed first-principles analysis of the electronic structures of oxygen defective CeO2 and Cu/CeO2 surfaces aimed at elucidating the disappearance of the gap state of defective CeO2 when a Cu atom is added at the surface. The top of the valence band of Cu/CeO2 originates from the O 2p states around this Cu atom. We show that this redistribution of electronic states at the defective Cu/CeO2 surface enhances the reactivity of the surface O atoms. Indeed, dynamical simulations show an acceleration of catalytic NO oxidation occurring via the Mars-van Krevelen mechanism mediated by these highly reactive oxygens.

Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes.

To elucidate how the nylon oligomer hydrolase (NylB) acquires its peculiar degradation activity towards non-biological amide bonds, we inspected the underlying enzymatic processes going from the induced-fit upon substrate binding to acylation. Specifically we investigated the mutational effects of two mutants, Y170F and D181G, indicated in former experiments as crucial systems because of their specific amino acid residues. Therefore, by adopting first-principles molecular dynamics complemented with metadynamics we provide a detailed insight into the underlying acylation mechanism. Our results show that while in the wild type (WT) the Tyr170 residue points the NH group towards the proton-acceptor site of an artificial amide bond, hence ready to react, in the Y170F this does not occur. The reason is ascribed to the absence of Tyr170 in the mutant, which is replaced by phenylalanine, which is unable to form hydrogen bond with the amide bond; thus, resulting in an increase in the activation barrier of more than 10 kcal mol(-1). Nonetheless, despite the lack of hydrogen bonding between the Y170F and the substrate, the highest free energy barrier for the induced-fit is similar to that of WT. This seems to suggest that in the induced-fit process, kinetics is little affected by the mutation. On the basis of additional structural homology analyses on the enzymes of the same family, we suggest that natural selection is responsible for the development of the peculiar hydrolytic activity of Arthrobacter sp. KI72.