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.

Origin of Homochirality in Amino Acids Induced by Lyman-α Irradiation in the Early Stage of the Milky Way.

The enantiomeric excess (ee) of l-form amino acids found in the Murchison meteorite poses some issues about the cosmic origin of their chirality. Circular dichroism (CD) spectra of amino acids in the far-ultraviolet (FUV) at around 6.8 eV (182 nm) indicate that the circularly polarized light can induce ee through photochemical reactions. Here, we resort to ab initio calculations to extract the CD spectra up to the vacuum-ultraviolet (VUV) region (∼11 eV), and we propose a novel equation to compute the ee applicable to a wider range of light frequency than what is available to date. This allows us to show that the strength of the induced ee (|ee|) in the 10 eV VUV region is comparable to the one in the 6.8 eV FUV region. This feature is common for some key amino acids (alanine, 2-aminobutyric acid, and valine). In space, intense Lyman-α (Lyα) light of 10.2 eV is emitted from star forming regions. This study provides a theoretical basis that Lyα emitter from an early starburst in the Milky Way plays a crucial role in initiating the ee of amino acids.

Hierarchical Self-Assembly and Conformation of Tb Double-Decker Molecular Magnets: Experiment and Molecular Dynamics.

Nanostructures, fabricated by locating molecular building blocks in well-defined positions, for example, on a lattice, are ideal platforms for studying atomic-scale quantum effects. In this context, STM data obtained from self-assembled Bis(phthalocyaninato) Terbium (III) (TbPc2) single-molecule magnets on various substrates have raised questions about the conformation of the TbPc2 molecules within the lattice. In order to address this issue, molecular dynamics simulations were carried out on a 2D assembly of TbPc2 molecules. The calculations are in excellent agreement with the experiment, and thus improve our understanding of the self-assembly process. In particular, the calculated electron density of the molecular assembly compares well with STM contrast of self-assembled TbPc2 on Au(111), simultaneously providing the conformation of the two Pc ligands of the individual double-decker molecule. This approach proves valuable in the identification of the STM contrast of LnPc2 layers and could be used in similar cases where it is difficult to interpret the STM images of an assembly of molecular complexes.

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.

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.

Enantiomeric Excesses of Aminonitrile Precursors Determine the Homochirality of Amino Acids.

High enantiomeric excesses (ee's) of l-amino acids, including non-proteinogenic amino acid isovaline (Iva), were discovered in the Murchison meteorite, but the detailed molecular mechanism responsible for the observed ee of amino acids remains elusive and inconsistent, because Iva has an inverted circular dichroism (CD) spectrum with respect to α-H amino acids, e.g., alanine. To address this issue, we resort to accurate ab initio calculations for amino acids and their precursors in the Strecker synthesis. We evaluated their photolysis-induced ee in the range 5-11 eV including the Lyman alpha emission line (Lyα), the typical intensive 10.2 eV radiation ascribed to the early phase of galactic evolution. We show that only the aminonitrile precursors are characterized by positive ee in the Lyα region, explaining why right-handed circularly polarized Lyα (R-CP-Lyα) induces homologous l-amino acids. This study shows that the homochirality of amino acids is produced at the aminonitrile precursors stage.

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.

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.

Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase.

Copper amine oxidase from Arthrobacter globiformis (AGAO) catalyses the oxidative deamination of primary amines via a large conformational change of a topaquinone (TPQ) cofactor during the semiquinone formation step. This conformational change of TPQ occurs in the presence of strong hydrogen bonds and neighboring bulky amino acids, especially the conserved Asn381, which restricts TPQ conformational changes over the catalytic cycle. Whether such a semiquinone intermediate is catalytically active or inert has been a matter of debate in copper amine oxidases. Here, we show that the reaction rate of the Asn381Ala mutant decreases 160-fold, and the X-ray crystal structures of the mutant reveals a TPQ-flipped conformation in both the oxidized and reduced states, preceding semiquinone formation. Our hybrid quantum mechanics/molecular mechanics (QM/MM) simulations show that the TPQ conformational change is realized through the sequential steps of the TPQ ring-rotation and slide. We determine that the bulky side chain of Asn381 hinders the undesired TPQ ring-rotation in the oxidized form, favoring the TPQ ring-rotation in reduced TPQ by a further stabilization leading to the TPQ semiquinone form. The acquired conformational flexibility of TPQ semiquinone promotes a high reactivity of Cu(i) to O2, suggesting that the semiquinone form is catalytically active for the subsequent oxidative half-reaction in AGAO. The ingenious molecular mechanism exerted by TPQ to achieve the "state-specific" reaction sheds new light on a drastic environmental transformation around the catalytic center.

Comprehensive Search of Stable Isomers of Alanine and Alanine Precursors in Prebiotic Syntheses.

Enantiomeric excesses of l-amino acids have been detected in meteorites; however, their molecular mechanism and prebiotic syntheses are still a matter of debate. To elucidate the origin of homochirality, alanine and the chiral precursors formed in prebiotic processes were investigated with regard to their stabilities among their isomers by employing the minimum energy principle, namely, the abundancy of a molecule in the interstellar medium is directly correlated to the stability among isomers. To facilitate the search for possible isomers, we developed a new isomer search algorithm, the random connection method, and performed a thorough search for all the stable isomers within a given chemical formula. We found that alanine and most of its precursors are located at higher energy by more than 5.7 kcal mol-1, with respect to the most stable isomer that consists of a linear-chain structure, whereas only the 2-aminopropanenitrile is the most stable isomer among all others possible. The inherent stability of the α-amino nitrile suggests that the 2-aminopropanenitrile is the dominant contribution in the formation of the common enantiomeric excess over α-amino acids.

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.

Estimation of the relative contributions to the electronic energy transfer rates based on Förster theory: The case of C-phycocyanin chromophores.

In the present study, we provide a reformulation of the theory originally proposed by Förster which allows for simple and convenient formulas useful to estimate the relative contributions of transition dipole moments of a donor and acceptor (chemical factors), their orientation factors (intermolecular structural factors), intermolecular center-to-center distances (intermolecular structural factors), spectral overlaps of absorption and emission spectra (photophysical factors), and refractive index (material factor) to the excitation energy transfer (EET) rate constant. To benchmark their validity, we focused on the EET occurring in C-phycocyanin (C-PC) chromophores. To this aim, we resorted to quantum chemistry calculations to get optimized molecular structures of the C-PC chromophores within the density functional theory (DFT) framework. The absorption and emission spectra, as well as transition dipole moments, were computed by using the time-dependent DFT (TDDFT). Our method was applied to several types of C-PCs showing that the EET rates are determined by an interplay of their specific physical, chemical, and geometrical features. These results show that our formulas can become a useful tool for a reliable estimation of the relative contributions of the factors regulating the EET transfer rate.

How natural materials remove heavy metals from water: mechanistic insights from molecular dynamics simulations.

Water pollution by heavy metals is of increasing concern due to its devastating effects on the environment and on human health. For the removal of heavy metals from water sources, natural materials, such as spent-coffee-grains or orange/banana/chestnut peels, appear to offer a potential cheap alternative to more sophisticated and costly technologies currently in use. However, in order to employ them effectively, it is necessary to gain a deeper understanding - at the molecular level - of the heavy metals-bioorganic-water system and exploit the power of computer simulations. As a step in this direction, we investigate via atomistic simulations the capture of lead ions from water by hemicellulose - the latter being representative of the polysaccharides that are common components of vegetables and fruit peels - as well as the reverse process. A series of independent molecular dynamics simulations, both classical and ab initio, reveals a coherent scenario which is consistent with what one would expect of an efficient capture, i.e. that it be fast and irreversible: (i) binding of the metal ions via adsorption is found to happen spontaneously on both carboxylate and hydroxide functional groups; (ii) in contrast, metal ion desorption, leading to solvation in water, involves sizable free-energy barriers.

First-principles thermal transport in amorphous Ge2Sb2Te5 at the nanoscale.

Achieving a precise understanding of nanoscale thermal transport in phase change materials (PCMs), such as Ge2Sb2Te5 (GST), is the key of thermal management in nanoelectronics, photonic and neuromorphic applications using non-volatile memories. By resorting to a first-principles approach to calculate the thermal conductivity of amorphous GST, we found that size effects and heat transport via propagative modes persist well beyond extended range order distances typical of disordered network-forming materials. Values obtained are in quantitative agreement with the experimental data, by revealing a strong size dependence of the thermal conductivity down to the 1.7-10 nm range, fully covering the scale of current PCMs-based devices. In particular, a reduction of thermal conductivity as large as 75% occurs for dimensions lying below 2 nm. These results provide a quantitative description of the thermal properties of amorphous GST at the nanoscale and are expected to underpin the development of PCM-based device applications.

Atomic Structure of Glassy GeTe4 as a Playground to Assess the Performances of Density Functional Schemes Accounting for Dispersion Forces.

The atomic structure of glassy GeTe4 is obtained in the framework of first-principles molecular dynamics (FPMD) by considering five different approaches for the description of the electronic structure within density functional theory (DFT). Among these schemes, one is not corrected by accounting for the dispersion forces and it is based on the BLYP exchange-correlation (XC) functional, while all of the others consider the dispersion forces according to different theoretical strategies. In particular, by maintaining the BLYP expression for the XC functional, two of them (BLYP-D2 and BLYP-D3) exploit the Grimme expressions for the dispersion forces, while the fourth scheme is based on the maximally localized Wannier functions (MLWFs). Finally, we also considered the rVV10 functional constructed to include seamlessly the dispersion part. Our results point out the better performances of BLYP-D3 and MLWF in terms of comparison with experimental data for the total pair correlation functions, with BLYP-D2 and rVV10 being closer to the uncorrected BLYP data. The implications of such findings are discussed by considering the overall limited impact of dispersion forces on the atomic structure of glassy GeTe4.

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.

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.

Unique protonation states of aspartate and topaquinone in the active site of copper amine oxidase.

The oxidative deamination of biogenic amines, crucial in the metabolism of a wealth of living organisms, is catalyzed by copper amine oxidases (CAOs). In this work, on the ground of accurate molecular modeling, we provide a clear insight into the unique protonation states of the key catalytic aspartate residue Asp298 and the prosthetic group of topaquinone (TPQ) in the CAO of Arthrobacter globiformis (AGAO). This provides both extensions and complementary information to the crystal structure determined by our recent neutron diffraction (ND) experiment. The hybrid quantum mechanics/molecular mechanics (QM/MM) simulations suggest that the ND structure closely resembles a state in which Asp298 is protonated and the TPQ takes an enolate form. The TPQ keto form can coexist in the fully protonated state. The energetic and structural analyses indicate that the active site structure of the AGAO crystal is not a single state but rather a mixture of the different protonation and conformational states identified in this work.

Screening the 4f-electron spin of TbPc2 single-molecule magnets on metal substrates by ligand channeling.

Bis(phthalocyaninato)lanthanide (LnPc2) double-decker-based devices have recently attracted a great deal of interest for data encoding purposes. Although the 4f-electrons of lanthanide ions play a key role in the experimental methodology, their localized character, deeper in energy compared to the 3d electrons of transition metals, hampers a detailed investigation. Here, our approach consists of the follow-up of the entanglement process with other molecules and with the substrate electrons by means of space-resolved detection of the Kondo resonance by scanning tunneling spectroscopy (STS), using different substrates (from weak to strong interaction). It is found that TbPc2 molecules firstly interact with their environment by means of the π-radicals of the ligand. The radical spin of TbPc2 can be identified by STS on a weakly interacting substrate such as Au(111). In the case of a Ag(111) substrate, we are able to analyze the effect of an electron transfer on the molecule (pairing-up of the radical spin) and the subsequent quenching of the Kondo resonance. Finally, on a strongly interacting substrate such as Cu(111), a significant rearrangement of electrons takes place and the Kondo screening of the 4f electrons of the Tb ion of TbPc2 is observed. By comparative STS measurements on YPc2, that has empty 4d and 4f shells, we prove that the Kondo resonance measured in the center of the TbPc2 molecule indeed stems from the 4f-electrons. At the same time, we provide evidence for the hybridization of the 4f states with the π electron.