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Accurate spectroscopic parameters of isopropyl alcohol, a volatile organic compound present on Earth and in extraterrestrial atmospheres, are provided. The work pursues the study of the far-infrared region, describing the distribution of the low-lying vibrational energy levels that can be populated at very low temperatures, having effects on the detectability and identification. The potential energy surface shows 27 almost equivalent minima producing 27 subcomponents of the levels due to tunneling effects. Computations have been performed using highly correlated ab initio calculations, accurate enough to distinguish between the rotational parameters of the two quasi-identical conformers gauche and trans. A variational procedure in three dimensions depending on three interacting internal rotations, the internal rotation of the two methyl groups and the internal rotation of the hydroxyl group, is employed to compute the energies. The 27 subcomponents of the ground vibrational state can be grouped into three series of nine energy levels located around 0.000, 1.693, and 81.927 cm−1 whose energy difference is due to the OH torsion effect. The nine subcomponents integrated in each series derive from the torsion of the two methyl groups. The computations reproduce accurately the available experimental data. New predicted properties can help the spectroscopic analysis of the rotational-vibrational spectra in the gas phase and further detections of vibrationally excited isopropyl alcohol.

Catalytic cancer therapy targets cancer cells by exploiting the specific characteristics of the tumor microenvironment (TME). TME-based catalytic strategies rely on the use of molecules already present in the TME. Amino groups seem to be a suitable target, given the abundance of proteins and peptides in biological environments. Here we show that catalytic CuFe2O4 nanoparticles are able to foster transaminations with different amino acids and pyruvate, another key molecule present in the TME. We observed a significant in cellulo decrease in glutamine and alanine levels up to 48 h after treatment. In addition, we found that di- and tripeptides also undergo catalytic transamination, thereby extending the range of the effects to other molecules such as glutathione disulfide (GSSG). Mechanistic calculations for GSSG transamination revealed the formation of an imine between the oxo group of pyruvate and the free −NH2 group of GSSG. Our results highlight transamination as alternative to the existing toolbox of catalytic therapies.

Thermal and electronic transport properties are the keys to many technological applications of materials. Thermoelectric, TE, materials can be considered a singular case in which not only one but three different transport properties are combined to describe their performance through their TE figure of merit, ZT. Despite the availability of high-throughput experimental techniques, synthesizing, characterizing, and measuring the properties of samples with numerous variables affecting ZT are not a cost- or time-efficient approach to lead this strategy. The significance of computational materials science in discovering new TE materials has been running in parallel to the development of new frameworks and methodologies to compute the electron and thermal transport properties linked to ZT. Nevertheless, the trade-off between computational cost and accuracy has hindered the reliable prediction of TE performance for large chemical spaces. In this work, we present for the first time the combination of new ab initio methodologies to predict transport properties with machine learning and a high-throughput framework to establish a solid foundation for the accurate prediction of thermal and electron transport properties. This strategy is applied to a whole family of materials, binary skutterudites, which are well-known as good TE candidates. Following this methodology, it is possible not only to connect ZT with the experimental synthetic (carrier concentration and grain size) and operando (temperature) variables but also to understand the physical and chemical phenomena that act as driving forces in the maximization of ZT for p-type and n-type binary skutterudites.

Silica-supported phosphoric acid and metal phosphate catalyzed 1,3-butadiene (BDE) production from 2,3-butanediol (2,3-BDO) was studied using experimental and computational techniques. The catalyst was initially tested in a continuous flow reactor using commercially available 2,3-BDO, leading to maximum BDE yields of 63C%. Quantum chemical mechanistic studies revealed 1,2-epoxybutane is a kinetically viable and thermodynamically stable intermediate, supported by experimental demonstration that this epoxide can be converted to BDE under standard reaction conditions. Newly proposed E2 and SN2′ elementary steps were studied to rationalize the formation of BDE and all detected side-products. Additionally, using quantum mechanics/molecular mechanics (QM/MM) calculations, we modeled silica-supported phosphate catalysts to study the effect of the alkali metal center. Natural population analysis showed that phosphate oxygen atoms are more negatively charged in CsH2PO4/SiO2 than in H3PO4/SiO2. In combination with temperature-programmed desorption experiments using CO2, the results of this study suggest that the improved selectivity achieved when adding the metal center is related to an increase in the basicity of the catalyst.

Solid-state electrolytes (SSEs) with high ion conductivity are pivotal for the development and large-scale adoption of green-energy conversion and storage technologies such as fuel cells, electrocatalysts and solid-state batteries. Yet, SSEs are extremely complex materials for which general rational design principles remain indeterminate. Here, we combine first-principles materials modelling, computational power and modern data analysis techniques to advance towards the solution of such a fundamental and technologically pressing problem. Our data-driven survey reveals that the correlations between ion diffusivity and other materials descriptors in general are monotonic, although not necessarily linear, and largest when the latter are of vibrational nature and explicitly incorporate anharmonic effects. Surprisingly, principal component and k-means clustering analyses show that elastic and vibrational descriptors, rather than the usual ones related to chemical composition and ion mobility, are best suited for reducing the high complexity of SSEs and classifying them into universal classes. Our findings highlight the need for considering databases that incorporate temperature effects to improve our understanding of SSEs and point towards a generalized approach to the design of energy materials.

Density functional theory (DFT) is applied to theoretically study the capture and storage of three different nitro polycyclic aromatic hydrocarbons, 4-Nitrophenol, 2-Nitrophenol and 9-Nitroanthracene by activated carbon, with and without the presence of water. These species are pollutants derived from vehicles and industry emissions. The modeling of adsorption is carried out at the molecular level using high level density functional theory with the B3LYP-GD(BJ)/6-31+G(d,p) level of theory. The adsorption energies of polluting gases considered isolated and in a humid environment are compared to better understanding the role of water. The calculations reveal different possible pathways involving the formation of chemicals bonds between adsorbent and adsorbate on the formation of intermolecular Van der Waals interactions. The negative adsorption energy on AC for the three species is obtained when they are treated individually and in mixture with H2O. The basis-set superposition error, estimated using the counterpoise correction, varies the adsorption energies by 2 to 13%. Dispersion effects were also taken into account. The adsorption energy ranges from -10 kJ/mol to -414 kJ/mol suggesting a diversity of pathways. The resulting analysis suggests three prefered pathways for catupre. The main pathway is physical interaction due to ¿-¿ stacking. Other means are capture due to the formation of hydrogen bonds resulting from water adsorbed on the surface, and the simultaneous adsorption of pollutant and water where water can act as a link that promotes adsorption. The thermodynamic properties give a clue to the most eco-friendly approaches for molecular adsorption.

Solid-state cooling applications based on electrocaloric (EC) effects are particularly promising from a technological point of view due to their downsize scalability and natural implementation in circuitry. However, EC effects typically involve materials that contain toxic substances and require relatively large electric fields (∼100-1000 kV cm-1) that cause fateful leakage current and dielectric loss problems. Here, we propose a possible solution to these practical issues that consists of concertedly applying hydrostatic pressure and electric fields on lead-free multiferroic materials. We theoretically demonstrate this strategy by performing first-principles simulations on supertetragonal BiFe1-xCoxO3 solid solutions (BFCO). It is shown that hydrostatic pressure, besides adjusting the occurrence of EC effects to near room temperature, can reduce enormously the intensity of driving electric fields. For pressurized BFCO, we estimate a colossal room-temperature EC strength, defined as the ratio of the adiabatic EC temperature change by an applied electric field, of ∼1 K cm kV-1, a value that is several orders of magnitude larger than those routinely measured in uncompressed ferroelectrics.

A recent experimental work on palladium hydrides suggested that metastable structures with hydrogen atoms occupying tetrahedral sites could lead to superconductivity above 50 K, a huge increase compared to the 9 K critical temperature of the stable structure with all hydrogen atoms occupying octahedral sites. By generating many structures with hydrogen atoms randomly occupying the octahedral and tetrahedral sites of the face-centered-cubic lattice and calculating their energy at different theoretical levels from first principles, we determine that metastable structures with partial or full occupation of tetrahedral sites are possible, even when the ionic quantum zero-point energy and anharmonicity are included in the calculations. Anharmonicity is crucial in palladium hydrides when hydrogen atoms occupy octahedral sites and, in fact, makes the structure with full octahedral occupation the ground state. Despite the metastable existence of structures with full or partial tetrahedral site occupation, the superconducting critical temperature is reduced with the number of tetrahedral sites occupied. Our calculations discard that the occupation of tetrahedral sites can increase the critical temperature in palladium hydrides.

Imidazole glycerol phosphate synthase (IGPS) is a class-I glutamine amidotransferase (GAT) that hydrolyzes glutamine. Ammonia is produced and transferred to a second active site, where it reacts with N1-(5′-phosphoribosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) to form precursors to purine and histidine biosynthesis. Binding of PrFAR over 25 Å away from the active site increases glutaminase efficiency by ∼4500-fold, primarily altering the glutamine turnover number. IGPS has been the focus of many studies on allosteric communication; however, atomic details for how the glutamine hydrolysis rate increases in the presence of PrFAR are lacking. We present a density functional theory study on 237-atom active site cluster models of IGPS based on crystallized structures representing the inactive and allosterically active conformations and investigate the multistep reaction leading to thioester formation and ammonia production. The proposed mechanism is supported by similar, well-studied enzyme mechanisms, and the corresponding energy profile is consistent with steady-state kinetic studies of PrFAR + IGPS. Additional active site models are constructed to examine the relationship between active site structural change and transition-state stabilization via energy decomposition schemes. The results reveal that the inactive IGPS conformation does not provide an adequately formed oxyanion hole structure and that repositioning of the oxyanion strand relative to the substrate is vital for a catalysis-competent oxyanion hole, with or without the hVal51 dihedral flip. These findings are valuable for future endeavors in modeling the IGPS allosteric mechanism by providing insight into the atomistic changes required for rate enhancement that can inform suitable reaction coordinates for subsequent investigations.

The (H2CO)2 +OH and H2CO-OH+H2CO reaction dynamics are studied theoretically for temperatures below 300 K. For this purpose, a full dimension potential energy surface is built, which reproduces well accurate ab initio calculations. The potential presents a submerged reaction barrier, as an example of the catalytic effect induced by the presence of the third molecule. However, quasi-classical and ring polymer molecular dynamics calculations show that the dominant channel is the dimer-exchange mechanism below 200 K, and that the reactive rate constant tends to stabilize at low temperatures, because the effective dipole of either dimer is reduced with respect to that of formaldehyde alone. The reaction complex formed at low temperatures does not live long enough to produce complete energy relaxation, as assumed in statistical theories. These results show that the reactivity of the dimers cannot explain the large rate constants measured at temperatures below 100 K.

The formation of vapor bubbles in a metastable liquid, cavitation, is an activated process due to the free energy cost of having both phases at contact. Such an energetic penalty enables the existence of the liquid beyond its thermodynamic borders. Establishing the stability limits of a liquid as ubiquitous as water has important practical implications and has thereby attracted a lot of attention. Different experimental strategies and theoretical analyses have been employed to measure and predict the cavitation line, or the pressure-temperature kinetic stability border of liquid water. Understanding the location of the cavitation line requires knowing the cavitation rate dependence on pressure and temperature. Such dependency is difficult to obtain in experiments, and we use molecular simulations with the TIP4P/2005 model to fill this gap. By deeply overstretching liquid water below the saturation pressure, we are able to observe and quantify spontaneous cavitation. To deal with a lower overstretching regime, we resort to the Seeding technique, which consists of analyzing simulations of a liquid containing a vapor bubble under the theoretical framework of Classical Nucleation Theory. Combining spontaneous cavitation with Seeding, we get a wide overview of the cavitation rate. We study two different temperatures (450 and 550 K) and complement our perspective with the results previously obtained at 296.4 K [Menzl et al., Proc. Natl. Acad. Sci. 113, 13582 (2016)] to establish a broad simulation-experiment comparison. We find a good agreement between simulations and both isobaric heating and isochoric cooling experiments using quartz inclusions. We are, however, unable to reconcile simulations with other experimental techniques. Our results predict a decrease in the solid-liquid interfacial free energy as the liquid becomes increasingly overstretched with a temperature independent Tolman length of 0.1 nm. Therefore, the capillarity approximation underestimates the nucle

Nanostructuring is a well-established approach to improve the thermoelectric behavior of materials. However, its effectiveness is restricted if excessively small particle sizes are necessary to considerably decrease the lattice thermal conductivity. Furthermore, if the electrical conductivity is unfavorably affected by the nanostructuring, it could cancel out the advantages of this approach. Computer simulations predict that silver indium telluride, AgInTe2, is unique among chalcopyrite-structured chalcogenides in requiring only a mild reduction of particle size to achieve a substantial reduction in lattice thermal conductivity. Here, ab initio calculations and machine learning are combined to systematically chart the thermoelectric properties of nanostructured AgInTe2, in comparison with its Cu-based counterpart, CuInTe2. In addition to temperature and doping carrier concentration dependence, ZT is calculated for both materials as functions of the polycrystalline average grain size, taking into account the effect of nanostructuring on both phonon and electron transport. It is shown that the different order of magnitude between the mean free path of electrons and phonons disentangles the connection between the power factor and lattice thermal conductivity when reducing the crystal size. ZT values up to 2 are predicted for p-type AgInTe2 at 700 K when the average grain size is in the affordable 10–100 nm range.

We evidence the possibility for coherent electrical manipulation of the spin orientation of topologically protected edge states in a low-symmetry quantum spin Hall insulator. By using a combination of ab initio simulations, symmetry-based modeling, and large-scale calculations of the spin Hall conductivity, it is shown that small electric fields can efficiently vary the spin textures of edge currents in monolayer 1T'-WTe2 by up to a 90-degree spin rotation, without jeopardizing their topological character. These findings suggest a new kind of gate-controllable spin-based device, topologically protected against disorder and of relevance for the development of topological spintronics.

Genomic reference databases of residing populations are available in different countries and regions. Since they represent the whole genetic diversity of a geographical region, they have wide applications, from biomedical studies to forensic identifications. Uniparentally transmitted portions of the genome specifically are highly suitable for kinship analyses, mixed DNA cases and geographical ancestry inferences. We have sampled 808 individuals currently residing in Catalonia within the GCAT cohort, from which we have generated 808 high-quality whole mitochondrial DNA (mtDNA) genomes and 399 sequences of the male-specific part of the Y chromosome (MSY). We observe higher genetic diversity than in classical population genetics datasets. We test the robustness of whole sequences for unequivocal identifications, and we found that they have higher resolution than mitochondrial control region and Y chromosome short tandem repeats (Y-STRs), and that most of the variants they present are at low frequencies, increasing the discrimination capacity between individuals. These results confirm the forensic applicability of whole uniparental sequences and provide one of the largest high-quality reference datasets ever published.

Background: Acetone is present in the earths atmosphere and extra-terrestrially. The knowledge of its chemical history in these environments represents a challenge with important implications for global tropospheric chemistry and astrochemistry. The results of a search for efficient barrierless pathways producing acetone from radicals in the gas phase are described in this paper. The spectroscopic properties of radicals needed for their experimental detection are provided. Methods: The reactants were acetone fragments of low stability and small species containing C, O and H atoms. Two exergonic bimolecular addition reactions involving the radicals CH 3, CH 3CO, and CH 3COCH 2, were found to be competitive according to the kinetic rates calculated at different temperatures. An extensive spectroscopic study of the radicals CH 3COCH 2 and CH 3CO, as well as the CH 2CHO isomer, was performed. Rovibrational parameters, anharmonic vibrational transitions, and excitations to the low-lying excited states are provided. For this purpose, RCCSD(T)-F12 and MRCI/CASSCF calculations were performed. In addition, since all the species presented non-rigid properties, a variational procedure of reduced dimensionality was employed to explore the far infrared region. Results: The internal rotation barriers were determined to be V 3=143.7 cm -1 (CH 3CO), V 2=3838.7 cm -1 (CH 2CHO) and V 3=161.4 cm -1 and V 2=2727.5 cm -1 (CH 3COCH 2).The splitting of the ground vibrational state due to the torsional barrier have been computed to be 2.997 cm -1, 0.0 cm -1, and 0.320 cm -1, for CH 3CO, CH 2CHO, and CH 3COCH 2, respectively. Conclusions: Two addition reactions, H+CH 3COCH 2 and CH 3+CH 3CO, could be considered barrierless formation processes of acetone after considering all the possible formation routes, starting from 58 selected reactants, which are fragments of the molecule. The spectroscopic study of the radicals involved in the formation processes present non-rigidity. The interconvers

Salt aqueous solutions are relevant in many fields, ranging from biological systems to seawater. Thus, the availability of a force-field that is able to reproduce the thermodynamic and dynamic behavior of salt aqueous solutions would be of great interest. Unfortunately, this has been proven challenging, and most of the existing force-fields fail to reproduce much of their behavior. In particular, the diffusion of water or the salt solubility are often not well reproduced by most of the existing force-fields. Recently, the Madrid-2019 model was proposed, and it was shown that this force-field, which uses the TIP4P/2005 model for water and non-integer charges for the ions, provides a good description of a large number of properties, including the solution densities, viscosities, and the diffusion of water. In this work, we assess the performance of this force-field on the evaluation of the freezing point depression. Although the freezing point depression is a colligative property that at low salt concentrations depends solely on properties of pure water, a good model for the electrolytes is needed to accurately predict the freezing point depression at moderate and high salt concentrations. The coexistence line between ice and several salt aqueous solutions (NaCl, KCl, LiCl, MgCl2, and Li2SO4) up to the eutectic point is estimated from direct coexistence molecular dynamics simulations. Our results show that this force-field reproduces fairly well the experimentally measured freezing point depression with respect to pure water freezing for all the salts and at all the compositions considered.

AntiMicrobial Resistance (AMR) is a worldwide health emergency. ESKAPE pathogens include the most relevant AMR bacterial families. In particular, Gram-negative bacteria stand out due to their cell envelope complexity which exhibits strong resistance to antimicrobials. A key element for AMR is the chemical structure of lipid A, modulating the physico-chemical properties of the membrane and permeability to antibiotics. Liposomes are used as models of bacterial membrane infective vesicles. In this work, coarse-grained molecular dynamics simulations were used to model liposomes from ESKAPE Gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa). We captured the role of lipid A, cardiolipin and cholesterol on liposome morphology and physico-chemical properties. Additionally, the reported antimicrobial peptides Cecropin B1, JB95, and PTCDA1-kf, were used to unveil their implications on membrane disruption. This study opens a promising starting point to understand molecular keys of bacterial membranes and to promote the discovery of new antimicrobials to overcome AMR.

[EN] Poly-Oxymethylene Dimethyl Ethers (OMEx) are being intensively investigated because of their potentially renewable synthesis path, which make them suitable as liquid fuels for low-carbon transport applications. In the present contribution, a computational study on the difference in combustion characteristics between dodecane and OMEx-type fuels under Engine Combustion Network (ECN) Spray A conditions is reported. In particular, a blend of different OMEx fuels have been investigated and compared to dodecane, which is a more conventional diesellike fuel. The modelling framework consists of a high-fidelity LES approach together with a Eulerian-Lagrangian spray model and flamelet-based turbulent combustion model. Results indicate ignition delay time and lift-off length according to the fuel reactivity properties, with the OMEx fuel performing similarly to dodecane. Flamelet calculations show that ignition of the oxygenated fuels is in general similar to that of dodecane, but it occurs at higher mixture fraction values due to the differences in stoichiometry. One of the most relevant outcomes of the study is the important effect that the oxygenated characteristics of OMEx has on the flame structure. Results show that for OMEx the reaction front is stabilized at distances closer to the nozzle than for dodecane, and that the flame shape as well as its internal structure is clearly affected.

The seeding method is an approximate approach to investigate nucleation that combines molecular dynamics simulations with classical nucleation theory. Recently, this technique has been successfully implemented in a broad range of nucleation studies. However, its accuracy is subject to the arbitrary choice of the order parameter threshold used to distinguish liquid-like from solid-like molecules. We revisit here the crystallization of NaCl from a supersaturated brine solution and show that consistency between seeding and rigorous methods, like Forward Flux Sampling (from previous work) or spontaneous crystallization (from this work), is achieved by following a mislabelling criterion to select such threshold (i.e. equaling the fraction of the mislabelled particles in the bulk parent and nucleating phases). This work supports the use of seeding to obtain fast and reasonably accurate nucleation rate estimates and the mislabelling criterion as one giving the relevant cluster size for classical nucleation theory in crystallization studies.

Antimicrobial resistance (AMR) represents a major threat to global public health in the 21st century, dramatically increasing the pandemic expectations in the coming years. The ongoing need to develop new antimicrobial treatments that are effective against multi-drug-resistant pathogens has led the research community to investigate innovative strategies to tackle AMR. The bacterial cell envelope has been identified as one of the key molecular players responsible for antibiotic resistance, attracting considerable interest as a potential target for novel antimicrobials effective against AMR, to be used alone or in combination with other drugs. However, the multicomponent complexity of bacterial membranes provides a heterogeneous morphology, which is typically difficult to study at the molecular level by experimental techniques, in spite of the significant development of fast and efficient experimental protocols. In recent years, computational modeling, in particular, molecular dynamics simulations, has proven to be an effective tool to reveal key aspects in the architecture and membrane organization of bacterial cell walls. Here, after a general overview about bacterial membranes, AMR mechanisms, and experimental approaches to study AMR, we review the state-of-the-art computational approaches to investigate bacterial AMR envelopes, including their limitations and challenges ahead. Representative examples illustrate how these techniques improve our understanding of bacterial membrane resistance mechanisms, hopefully leading to the development of novel antimicrobial drugs escaping from bacterial resistance strategies.

Quantum variational optimization has been posed as an alternative to solve optimization problems faster and at a larger scale than what classical methods allow. In this paper we study systematically the role of entanglement, the structure of the variational quantum circuit, and the structure of the optimization problem, in the success and efficiency of these algorithms. For this purpose, our study focuses on the variational quantum eigensolver (VQE) algorithm, as applied to quadratic unconstrained binary optimization (QUBO) problems on random graphs with tunable density. Our numerical results indicate an advantage in adapting the distribution of entangling gates to the problem's topology, specially for problems defined on low-dimensional graphs. Furthermore, we find evidence that applying conditional value at risk type cost functions improves the optimization, increasing the probability of overlap with the optimal solutions. However, these techniques also improve the performance of Ansätze based on product states (no entanglement), suggesting that a new classical optimization method based on these could outperform existing NISQ architectures in certain regimes. Finally, our study also reveals a correlation between the hardness of a problem and the Hamming distance between the ground- and first-excited state, an idea that can be used to engineer benchmarks and understand the performance bottlenecks of optimization methods.

Gas phase formation processes feasible at low temperatures are determined theoretically for 38 isomers obeying the C3O3H6 empirical formula, one of them, the simplest ketose dihydroxyacetone, has been observed in gas phase sources. A preliminary search for isomeric forms first targets ethoxy formic acid (C2H5-O-COOH) as the most stable isomer followed by lactic acid. Profiles corresponding to the minimum energy pathways reveal that the favored conformers of 14 of these isomers can be formed in the gas phase through 29 barrierless processes involving the OH∗, CH3O∗, HCO∗, CH3∗, CH2OH, HCOO∗, and OHCO∗ radicals, all of them observed in the interstellar medium. Kinetic rates are provided at 200, 298, and 500 K, confirming the suitability of 16 processes at low temperatures. Faster processes involve the OH hydroxyl radical whereas, to a lesser degree, the processes involving the HOCO radical and the methoxy methyl radical CH3O∗, are quite significant. Spectroscopic parameters (rovibrational and torsional) are obtained for methoxy acetic acid (CH3-O-CH2COOH) for which two low-lying isoenergetic conformers can be produced from the CH3OCH2∗ radical predicted to be a precursor of abundant observed molecules. Profiles and spectroscopic properties make methoxy acetic acid a good candidate to be detected in the gas phase of extraterrestrial sources.

CCSD(T)-F12 theory is applied to determine electronic ground state spectroscopic parameters of various isotopologues of methylamine (CH-NH) containing cosmological abundant elements, such as D, C and N. Special attention is given to the far infrared region. The studied isotopologues can be classified in the G, G and G molecular symmetry groups. The rotational and centrifugal distortion constants and the anharmonic fundamentals are determined using second order perturbation theory. Fermi displacements of the vibrational bands are predicted. The low vibrational energy levels corresponding to the large amplitude motions are determine variationally using a flexible three-dimensional model depending on the NH bending and wagging and the CH torsional coordinates. The model has been defined assuming that, in the amine group, the bending and the wagging modes interact strongly. The vibrational levels split into six components corresponding to the six minima of the potential energy surface. The accuracy of the kinetic energy parameters has an important effect on the energies. Strong interactions among the large amplitude motions are observed. Isotopic effects are relevant for the deuterated species.

The non-adiabatic quantum dynamics of the H + H2+ → H2 + H+ charge transfer reactions, and some isotopic variants, is studied with an accurate wave packet method. A recently developed 3 × 3 diabatic potential model is used, which is based on very accurate ab initio calculations and includes the long-range interactions for ground and excited states. It is found that for initial H2+(v = 0), the quasi-degenerate H2(v′ = 4) non-reactive charge transfer product is enhanced, producing an increase in the reaction probability and cross section. It becomes the dominant channel from collision energies above 0.2 eV, producing a ratio between v′ =4 and the rest of v's, which that increase up to 1 eV. The H + H2+ → H2+ + H exchange reactionchannel is nearly negligible, while the reactive and non-reactive charge transfer reaction channelsare of the same order, except that corresponding to H2(v′ = 4), and the two chargetransfer processes compete below 0.2 eV. This enhancement is expected to play an important vibrational and isotopic effect that needs to be evaluated. For the three proton case, the problem of the permutation symmetry is discussed when using reactant Jacobi coordinates.

The time-resolved photodynamics of the methyl iodide cation (CH3I+) are investigated by means of femtosecond XUV-IR pump-probe spectroscopy. A time-delay-compensated XUV monochromator is employed to isolate a specific harmonic, the 9th harmonic of the fundamental 800 nm (13.95 eV, 88.89 nm), which is used as a pump pulse to prepare the cation in several electronic states. A time-delayed IR probe pulse is used to probe the dissociative dynamics on the first excited state potential energy surface. Photoelectrons and photofragment ions - and I+ - are detected by velocity map imaging. The experimental results are complemented with high level ab initio calculations for the potential energy curves of the electronic states of CH3I+ as well as with full dimension on-the-fly trajectory calculations on the first electronically excited state, considering the presence of the IR pulse. The and I+ pump-probe transients reflect the role of the IR pulse in controlling the photodynamics of CH3I+ in the state, mainly through the coupling to the ground state and to the excited state manifold. Oscillatory features are observed and attributed to a vibrational wave packet prepared in the state. The IR probe pulse induces a coupling between electronic states leading to a slow depletion of fragments after the cation is transferred to the ground states and an enhancement of I+ fragments by absorption of IR photons yielding dissociative photoionization.

Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs.

A new potential energy surface (PES) and dynamical study of the reactive process of H2CO + OH toward the formation of HCO + H2O and HCOOH + H are presented. In this work, a source of spurious long range interactions in symmetry adapted neural network (NN) schemes is identified, which prevents their direct application for low temperature dynamical studies. For this reason, a partition of the PES into a diabatic matrix plus a NN many-body term has been used, fitted with a novel artificial neural network scheme that prevents spurious asymptotic interactions. Quasi-classical trajectory (QCT) and ring polymer molecular dynamics (RPMD) studies have been carried on this PES to evaluate the rate constant temperature dependence for the different reactive processes, showing good agreement with the available experimental data. Of special interest is the analysis of the previously identified trapping mechanism in the RPMD study, which can be attributed to spurious resonances associated with excitations of the normal modes of the ring polymer.

[EN] We report a joint experimental and theoretical study of the structural, vibrational, and electronic properties of layered monoclinic arsenic sulfide crystals (a-As2S3), aka mineral orpiment, under compression. X-ray diffraction and Raman scattering measurements performed on orpiment samples at high pressure and combined with ab initio calculations have allowed us to determine the equation of state and the tentative assignment of the symmetry of many Raman-active modes of orpiment. From our results, we conclude that no first-order phase transition occurs up to 25 GPa at room temperature; however, compression leads to an isostructural phase transition above 20 GPa. In fact, the As coordination increases from threefold at room pressure to more than fivefold above 20 GPa. This increase in coordination can be understood as the transformation from a solid with covalent bonding to a solid with metavalent bonding at high pressure, which results in a progressive decrease of the electronic and optical bandgap, an increase of the dielectric tensor components and Born effective charges, and a considerable softening of many high-frequency optical modes with increasing pressure. Moreover, we propose that the formation of metavalent bonding at high pressures may also explain the behavior of other group-15 sesquichalcogenides under compression. In fact, our results suggest that group-15 sesquichalcogenides either show metavalent bonding at room pressure or undergo a transition from p-type covalent bonding at room pressure towards metavalent bonding at high pressure, as a precursor towards metallic bonding at very high pressure.

Understanding the wetting properties of premelting films requires knowledge of the film's equation of state, which is not usually available. Here we calculate the disjoining pressure curve of premelting films and perform a detailed thermodynamic characterization of premelting behavior on ice. Analysis of the density profiles reveals the signature of weak layering phenomena, from one to two and from two to three water molecular layers. However, disjoining pressure curves, which closely follow expectations from a renormalized mean field liquid state theory, show that there are no layering phase transitions in the thermodynamic sense along the sublimation line. Instead, we find that transitions at mean field level are rounded due to capillary wave fluctuations. We see signatures that true first order layering transitions could arise at low temperatures, for pressures between the metastable line of water-vapor coexistence and the sublimation line. The extrapolation of the disjoining pressure curve above water-vapor saturation displays a true first order phase transition from a thin to a thick film consistent with experimental observations.

Surfactant-assisted seeded growth of metal nanoparticles (NPs) can be engineered to produce anisotropic gold nanocrystals with high chiroptical activity through the templating effect of chiral micelles formed in the presence of dissymmetric cosurfactants. Mixed micelles adsorb on gold nanorods, forming quasihelical patterns that direct seeded growth into NPs with pronounced morphological and optical handedness. Sharp chiral wrinkles lead to chiral plasmon modes with high dissymmetry factors (~0.20). Through variation of the dimensions of chiral wrinkles, the chiroptical properties can be tuned within the visible and near-infrared electromagnetic spectrum. The micelle-directed mechanism allows extension to other systems, such as the seeded growth of chiral platinum shells on gold nanorods. This approach provides a reproducible, simple, and scalable method toward the fabrication of NPs with high chiral optical activity.

The molecular magnets Cu(hfac)2LR based on copper(II) and pyrazolyl-substituted nitronyl nitroxide radicals LR exhibit thermally and optically-induced magnetostructural transitions, similar to the spin-crossover and light-induced excited spin state trapping phenomena. The mechanism of the gradual change of the magnetic moment in Cu(hfac)2LR remains unclear. Herewith, we report a detailed study of this mechanism at molecular level based on DDCI and periodic DFT+U calculations. Three representative members of the Cu(hfac)2LR family have been selected, with different substituents (R=Pr, Bu) and solvents (octane, o-xylane, without solvent). Our results indicate that the magnetostructural transition can be related to the coexistence of two limit structures, the low temperature (LT) phase with a strong coupling between the Cu(II) and nitronyl nitroxide spins and the high temperature (HT) phase, where the spins are weakly coupled. In this scenario, the gradual change of the magnetic moment with temperature just reflects the thermally weighted ratio of the two limit LT and HT phases. Our finding supports the changes observed on the variable temperature-FTIR spectra of Cu(hfac)2LPr, manifested by the increase/decrease of certain vibrational bands with temperature and suggest an unified mechanism governing the gradual magnetic anomalies of the Cu(hfac)2LR complexes.

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Sustainable Chemistry & Engineering, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acssuschemeng.8b04462", [EN] P-doped graphene (Phy-G) prepared by pyrolysis of phytic acid at 900 degrees C under inert atmosphere has been evaluated as a metal-free catalyst for the thermochemical water splitting. XPS, solid-state P-31 NMR, and Raman spectroscopy confirm the presence of P atoms bonded to C atoms in the graphene lattice as well as some oxygenated P groups, such as phosphates or phosphonates. HRTEM and AFM images show the characteristic sheet morphology of 2D graphene materials of several micrometers lateral size and exhibiting a high crystallinity with the characteristic hexagonal arrangement of graphenic materials. Phy-G has been submitted to consecutive oxidation/activation thermochemical cycles at 650 and 800 degrees C under H2O-saturated Ar and dry Ar atmospheres, respectively. During the oxidation periods, H-2 evolution up to 21.6 mu mol/min.g was measured. However, no O-2 evolves in the activation steps. Experimental evidence and computational calculations support the formation of P=O bonds during the oxidation steps. The computational calculations suggest that the thermocatalytic H2O splitting occurs on the P atoms of doped graphene through a stepwise process involving an intermediate with a P-OH group and a H attached to a neighboring C atom and subsequent H-2 evolution, leading to the formation of P-O bonds.

[EN] DNS of passive thermal turbulent Couette flow at several friction Reynolds numbers (180, 250, and 500), and the Prandtl number of air are presented. The time averaged thermal flow shows the existence of long and wide thermal structures never described before in Couette flows. These thermal structures, named CTFS (Couette Thermal Flow Superstructures), are defined as coherent regions of hot and cold temperature fluctuations. They are intrinsically linked to the velocity structures present in Couette flows. Two different 2D symmetries can be recognized, which get stronger with the Reynolds number. These structures do not affect the mean flow or mean quantities as the Nusselt number. However, turbulent intensities and thermal fluxes depend on the width of the structures, mainly far from the walls. Since the width of the structures is related to the channel width, the statistics of thermal Couette flow are to some point box-dependent.

The title reaction and its isotopic variants are studied using quasi-classical trajectory (QCT) (without taking into account corrections to account for the possible zero point energy breakdown) and ring polymer molecular dynamics (RPMD) methods with a full dimensional and accurate potential energy surface which presents an exchange barrier of approximately 0.144 eV. The QCT rate constant increases when the temperature decreases from 1500 to 10 K. On the contrary, the RPMD rate constant decreases with decreasing temperature, in semiquantitative agreement with recent experimental results. The present RPMD results are in between the thermal and translational experimental rate constants, extracted from the measured data to eliminate the initial vibrational excitation of H , obtained in an arc discharge. The difference between the present RPMD results and experimental values is attributed to the possible existence of non thermal vibrational excitation of H , not completely removed by the semiempirical model used for the analysis of the experimental results. Also, it is found that, below 200 K, the RPMD trajectories are trapped, forming long-lived collision complexes, with lifetimes longer than 1 ns. These collision complexes can fragment by either redissociating back to reactants or react to products, in the two cases tunneling through the centrifugal and reaction barriers, respectively. The contribution of the formation of the complex to the total deuteration rate should be calculated with more accurate quantum methods, as has been found recently for reactions of larger systems, and the present four atoms system is a good candidate to benchmark the adequacy of RPMD method at temperatures below 100 K.

The quantum dynamics of the title reactions are studied using the ring polymer molecular dynamics (RPMD) method from 20 to 1200 K using recently proposed full dimensional potential energy surfaces which include long-range dipole-dipole interactions. A V-shaped dependence of the reaction rate constants is found with a minimum at 200-300 K, in rather good agreement with the current experimental data. For temperatures above 300 K the reaction proceeds following a direct H-abstraction mechanism. However, below 100 K the reaction proceeds via organic-molecule···OH collision complexes, with very long lifetimes, longer than 10 s, associated with quantum roaming arising from the inclusion of quantum effects by the use of RPMD. The long lifetimes of these complexes are comparable to the time scale of the tunnelling to form reaction products. These complexes are formed at zero pressure because of quantum effects and not only at high pressure as suggested by transition state theory (TST) calculations for OH + methanol and other OH reactions. The zero-pressure rate constants reproduce quite well measured ones below 200 K, and this agreement opens the question of how important the pressure effects on the reaction rate constants are, as implied in TST-like formalisms. The zero-pressure mechanism is applicable only to very low gas density environments, such as the interstellar medium, which are not repeatable by experiments.

As proteins perform most cellular functions, quantitative understanding of protein energetics is required to gain control of biological phenomena. Accurate models of native proteins can be obtained experimentally, but the lack of equally fine models of unfolded ensembles impedes the calculation of protein folding energetics from first principles. Here, we show that an atomistic unfolded ensemble model, consisting of a few dozen conformations built from a protein sequence, can be used in conjunction with an X-ray structure of its native state to calculate accurately by difference the changes in enthalpy and heat capacity of the polypeptide upon folding. The calculation is done using molecular dynamics simulations, popular force fields, and water models, and for the two model proteins studied (barnase and SNase), the results agree within error or are very close to their experimentally determined properties. The enthalpy sampling of the unfolded ensemble is done through short 2 ns simulations that do not significantly modify the representative distribution of R of the starting conformations. The impressive accuracy obtained opens the possibility to investigate quantitatively systems or phenomena not amenable to experiment and paves the way for addressing the calculation of protein conformational stability (i.e., the change in Gibbs energy upon folding), a central goal of structural biology. So far, these calculated enthalpy and heat capacity changes, combined with the experimentally determined melting temperatures of the corresponding protein, allow us to reproduce the stability curves of both barnase and SNase.

One of the current challenges in nanoscience is tailoring the phononic properties of a material. This has long been a rather elusive task because several phonons have wavelengths in the nanometer range. Thus, high quality nanostructuring at that length-scale, unavailable until recently, is necessary for engineering the phonon spectrum. Here we report on the continuous tuning of the phononic properties of a twinning superlattice GaP nanowire by controlling its periodicity. Our experimental results, based on Raman spectroscopy and rationalized by means of ab initio theoretical calculations, give insight into the relation between local crystal structure, overall lattice symmetry, and vibrational properties, demonstrating how material engineering at the nanoscale can be successfully employed in the rational design of the phonon spectrum of a material.

The electronic structure and magnetic interactions of three representative members of the breathing crystal Cu(hfac)2LR family, mainly Cu(hfac)2LPr (1), Cu(hfac)2LBu·0.5C8H18 (2) and Cu(hfac)2LBu·0.5C8H10 (3), have been analyzed by means of periodic plane-wave based DFT+U calculations. These copper(II)-nitroxide based molecular magnets display promising thermally and optically induced switchable behaviour, similar to the spin-crossover and light-induced excited spin state trapping phenomena. The calculations confirm the presence of temperaturedependent exchange interaction within the spin triads formed by the three-spin nitronyl nitroxide-copper(II)-nitronyl nitroxide units, in line with the changes observed in the effective magnetic moment when temperature increases. Moreover, they quantify the interchain interaction mediated by the terminal nitroxide group of two spin triads in neighbour polymer chains. This interaction competes with the exchange interaction within the spin triads at high temperature and introduces 1D exchange channels that do not coincide with the polymeric chains. The density of states reveal that the low-lying conduction states potentially involved in the UV-vis transitions are mainly located on the nitronyl-nitroxide radicals, the hfac groups and the Cu atoms. Then, the density of states is almost independent of the solvent and the R group substituting the pyrazole moiety, which suggests the possibility of light-induced spin switching for other members of the breathing crystal family. The band at 500 nm characterizing the strongly-coupled low-temperature phase can be ascribed to a ligand-to-metal charge transfer transition between the nitronyl-nitroxide and the Cu bands. This study appears to be fundamental in order to properly understand the optical properties of these switching molecular magnets.

This work addresses the prediction of the reacting flow field in a swirl stabilized gas turbine model combustor using large-eddy simulation. The modeling of the combustion chemistry is based on laminar premixed flamelets and the effect of turbulence-chemistry interaction is considered by a presumed shape probability density function. The prediction capabilities of the presented combustion model for perfectly premixed and partially premixed conditions are demonstrated. The effect of partial premixing for the prediction of the reacting flow field is assessed by comparison of a perfectly premixed and partially premixed simulation. Even though significant mixture fraction fluctuations are observed, only small impact of the non-perfect premixing is found on the flow field and flame dynamics. Subsequently, the effect of heat loss to the walls is assessed assuming perfectly premixing. The adiabatic baseline case is compared to heat loss simulations with adiabatic and non-adiabatic chemistry tabulation. The results highlight the importance of considering the effect of heat loss on the chemical kinetics for an accurate prediction of the flow features. Both heat loss simulations significantly improve the temperature prediction, but the non-adiabatic chemistry tabulation is required to accurately capture the chemical composition in the reacting layers. © 2017, The Author(s).

In this report we present a systematic structural and magnetic analysis of Co-doped ZnO nanoparticles prepared via a microwave-assisted hydrothermal route. The structural data confirm the incorporation of Co ions into the wurtzite ZnO lattice and a Co concentration mainly near/at the surface of the nanoparticles. This Co spatial distribution is set to passivate the surface of the ZnO nanoparticles, inhibiting the nanoparticle growth and suppressing the observation of a ferromagnetic phase. Based on experimental and theoretical results we propose a kinetic-thermodynamic model for the processes of nucleation and growth of the Co-doped ZnO nanoparticles, and attribute the observed ferromagnetic order to a ferromagnetism associated with specific defects and adsorbed elements at the surface of the nanoparticle. Our findings give valuable contribution to the understanding of both the doping process at the nanoscale and the nature of the magnetic properties of the Co-doped ZnO system.

The characterization of the Galactic foregrounds has been shown to be the main obstacle in thechallenging quest to detect primordial B-modes in the polarized microwave sky. We make use of the Planck-HFI 2015 data release at high frequencies to place new constraints on the properties of the polarized thermal dust emission at high Galactic latitudes. Here, we specifically study the spatial variability of the dust polarized spectral energy distribution (SED), and its potential impact on the determination of the tensor-to-scalar ratio, r. We use the correlation ratio of the angular power spectra between the 217 and 353 GHz channels as a tracer of these potential variations, computed on different high Galactic latitude regions, ranging from 80% to 20% of the sky. The new insight from Planck data is a departure of the correlation ratio from unity that cannot be attributed to a spurious decorrelation due to the cosmic microwave background, instrumental noise, or instrumental systematics. The effect is marginally detected on each region, but the statistical combination of all the regions gives more than 99% confidence for this variation in polarized dust properties. In addition, we show that the decorrelation increases when there is a decrease in the mean column density of the region of the sky being considered, and we propose a simple power-law empirical model for this dependence, which matches what is seen in the Planck data. We explore the effect that this measured decorrelation has on simulations of the BICEP2-Keck Array/Planck analysis and show that the 2015 constraints from these data still allow a decorrelation between the dust at 150 and 353 GHz that is compatible with our measured value. Finally, using simplified models, we show that either spatial variation of the dust SED or of the dust polarization angle are able to produce decorrelations between 217 and 353 GHz data similar to the values we observe in the data.

Resonance states are interesting objects that can behave as intermediate or doorway states from which some molecular processes can be activated. Thus, controlling the decay process of a given resonance implies to control the molecular process mediated by that resonance state. The two essential observable properties associated with the decay of a resonance state are its lifetime and the final product fragment state distributions. Schemes to control the lifetime of a single resonance state have been developed for the cases of both overlapping (see Fig. 1, left panel) [1,2] and isolated [3] resonances. Control strategies to modify the product fragment state distributions produced by the decay of a superposition of resonances (see Fig. 1, right panel) [4-6], as well as of a single resonance [7], have also been proposed. A remarkably different behaviour is found depending upon whether the resonance state is completely isolated or overlapping with other resonances [7,8]. The different control schemes will be discussed.

Noble metal nanostructures dispersed on metal oxide surfaces have applications in diverse areas such as catalysis, chemical sensing, and energy harvesting. Their reactivity, chemical selectivity, stability, and light absorption properties are controlled by the interactions at the metal/oxide interface. Single-atom metal adsorbates on the rutile TiO(110)-(1 × 1) surface have become a paradigmatic model to characterize those interactions and to understand the unique electronic properties of these supported nanostructures. We combine Kelvin probe force microscopy (KPFM) experiments and density functional theory (DFT) calculations to investigate the atomic-scale variations in the contact potential difference of individual Pt atoms adsorbed on a hydroxylated (h) TiO(110)-(1 × 1) surface. Our experiments show a significant drop in the local contact potential difference (LCPD) over Pt atoms with respect to the TiO surface, supporting the presence of an electron transfer from the Pt adsorbates to the substrate. We have identified two characteristic regimes by LCPD spectroscopy. At far tip-sample distances, LCPD values show a weak distance dependence and can be attributed to the intrinsic charge transfer from Pt to the oxide support. Beyond the onset of short-range chemical interactions, LCPD values exhibit a strong distance dependence that we ascribe to the local structural and charge rearrangements induced by the tip-sample interaction. These findings also apply to other electropositive adsorbates such as potassium and the hydrogen atoms forming the OH groups that are present on the h-TiO(110) surface, promoting KPFM as a suitable tool for the understanding of electron transfer in catalytically active materials.