A Novel Abiotic Pathway for Phosphine Synthesis over Acidic Dust in Venus' Atmosphere.

Recent ground-based observations of Venus have detected a single spectral feature consistent with phosphine (PH3) in the middle atmosphere, a gas which has been suggested as a biosignature on rocky planets. The presence of PH3 in the oxidized atmosphere of Venus has not yet been explained by any abiotic process. However, state-of-the-art experimental and theoretical research published in previous works demonstrated a photochemical origin of another potential biosignature-the hydride methane-from carbon dioxide over acidic mineral surfaces on Mars. The production of methane includes formation of the HC · O radical. Our density functional theory (DFT) calculations predict an energetically plausible reaction network leading to PH3, involving either HC · O or H· radicals. We suggest that, similarly to the photochemical formation of methane over acidic minerals already discussed for Mars, the origin of PH3 in Venus' atmosphere could be explained by radical chemistry starting with the reaction of ·PO with HC·O, the latter being produced by reduction of CO2 over acidic dust in upper atmospheric layers of Venus by ultraviolet radiation. HPO, H2P·O, and H3P·OH have been identified as key intermediate species in our model pathway for phosphine synthesis.

The Reactivity-Enhancing Role of Water Clusters in Ammonia Aqueous Solutions.

Among the many prototypical acid-base systems, ammonia aqueous solutions hold a privileged place, owing to their omnipresence in various planets and their universal solvent character. Although the theoretical optimal water-ammonia molar ratio to form NH4+ and OH- ion pairs is 50:50, our ab initio molecular dynamics simulations show that the tendency of forming these ionic species is inversely (directly) proportional to the amount of ammonia (water) in ammonia aqueous solutions, up to a water-ammonia molar ratio of ∼75:25. Here we prove that the reactivity of these liquid mixtures is rooted in peculiar microscopic patterns emerging at the H-bonding scale, where the highly orchestrated motion of 5 solvating molecules modulates proton transfer events through local electric fields. This study demonstrates that the reaction of water with NH3 is catalyzed by a small cluster of water molecules, in which an H atom possesses a high local electric field, much like the effect observed in catalysis by water droplets [ PNAS 2023, 120, e2301206120].

Electric-field induced entropic effects in liquid water.

Externally applied electric fields in liquid water can induce a plethora of effects with wide implications in electrochemistry and hydrogen-based technologies. Although some effort has been made to elucidate the thermodynamics associated with the application of electric fields in aqueous systems, to the best of our knowledge, field-induced effects on the total and local entropy of bulk water have never been presented so far. Here, we report on classical TIP4P/2005 and ab initio molecular dynamics simulations measuring entropic contributions carried by diverse field intensities in liquid water at room temperature. We find that strong fields are capable of aligning large fractions of molecular dipoles. Nevertheless, the order-maker action of the field leads to quite modest entropy reductions in classical simulations. Albeit more significant variations are recorded during first-principles simulations, the associated entropy modifications are small compared to the entropy change involved in the freezing phenomenon, even at intense fields slightly beneath the molecular dissociation threshold. This finding further corroborates the idea that electrofreezing (i.e., the electric-field-induced crystallization) cannot take place in bulk water at room temperature. In addition, here, we propose a molecular-dynamics-based analysis (3D-2PT) that spatially resolves the local entropy and the number density of bulk water under an electric field, which enables us to map their field-induced changes in the environment of reference H2O molecules. By returning detailed spatial maps of the local order, the proposed approach is capable of establishing a link between entropic and structural modifications with atomistic resolution.

Electrofreezing of Liquid Ammonia.

Here we prove that, in addition to temperature and pressure, another important thermodynamic variable permits the exploration of the phase diagram of ammonia: the electric field. By means of (path integral) ab initio molecular dynamics simulations, we predict that, upon applying intense electric fields on ammonia, the electrofreezing phenomenon occurs, leading the liquid toward a novel ferroelectric solid phase. This study proves that electric fields can generally be exploited as the access key to otherwise-unreachable regions in phase diagrams, unveiling the existence of new condensed-phase structures. Furthermore, the reported findings have manifold practical implications, from the safe storage and transportation of ammonia to the understanding of the solid structures this compound forms in planetary contexts.

A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks.

The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter-including its quantum nature-under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schro¨dinger equation at different levels of approximation (i.e., density functional theory)-such as ab initio molecular dynamics-and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life.

Molecular dissociation and proton transfer in aqueous methane solution under an electric field.

Methane-water mixtures are ubiquitous in our solar system and they have been the subject of a wide variety of experimental, theoretical, and computational studies aimed at understanding their behaviour under disparate thermodynamic scenarios, up to extreme planetary ice conditions of pressures and temperatures [Lee and Scandolo, Nat. Commun., 2011, 2, 185]. Although it is well known that electric fields, by interacting with condensed matter, can produce a range of catalytic effects which can be similar to those observed when material systems are pressurised, to the best of our knowledge, no quantum-based computational investigations of methane-water mixtures under an electric field have been reported so far. Here we present a study relying upon state-of-the-art ab initio molecular dynamics simulations where a liquid aqueous methane solution is exposed to strong oriented static and homogeneous electric fields. It turns out that a series of field-induced effects on the dipoles, polarisation, and the electronic structure of both methane and water molecules are recorded. Moreover, upon increasing the field strength, increasing fractions of water molecules are not only re-oriented towards the field direction, but are also dissociated by the field, leading to the release of oxonium and hydroxyde ions in the mixture. However, in contrast to what is observed upon pressurisation (∼50 GPa), where the presence of the water counterions triggers methane ionisation and other reactions, methane molecules preserve their integrity up to the strongest field explored (i.e., 0.50 V Å-1). Interestingly, neither the field-induced molecular dissociation of neat water (i.e., 0.30 V Å-1) nor the proton conductivity typical of pure aqueous samples at these field regimes (i.e., 1.3 S cm-1) are affected by the presence of hydrophobic interactions, at least in a methane-water mixture containing a molar fraction of 40% methane.

Ab initio molecular dynamics simulations and experimental speciation study of levofloxacin under different pH conditions.

Levofloxacin is an extensively employed broad-spectrum antibiotic belonging to the fluoroquinolone class. Despite the extremely wide usage of levofloxacin for a plethora of diseases, the molecular characterization of this antibiotic appears quite poor in the literature. Moreover, the acid-base properties of levofloxacin - crucial for the design of efficient removal techniques from wastewaters - have never extensively been investigated so far. Here we report on a study on the behavior of levofloxacin under standard and diverse pH conditions in liquid water by synergistically employing static quantum-mechanical calculations along with experimental speciation studies. Furthermore, with the aim of characterizing the dynamics of the water solvation shells as well as the protonation and deprotonation mechanisms, here we present the unprecedented quantum-based simulation of levofloxacin in aqueous environments by means of state-of-the-art density-functional-theory-based molecular dynamics. This way, we prove the cooperative role played by the aqueous hydration shells in assisting the proton transfer events and, more importantly, the key place held by the nitrogen atom binding the methyl group of levofloxacin in accepting excess protons eventually present in water. Finally, we also quantify the energetic contribution associated with the presence of a H-bond internal to levofloxacin which, on the one hand, stabilizes the ground-state molecular structure of this antibiotic and, on the other, hinders the first deprotonation step of this fluoroquinolone. Among other things, the synergistic employment of quantum-based calculations and speciation experiments reported here paves the way toward the development of targeted removal approaches of drugs from wastewaters.

Electric-Field-Induced Effects on the Dipole Moment and Vibrational Modes of the Centrosymmetric Indigo Molecule.

Intense static electric fields can strongly perturb chemical bonds and induce frequency shifts of the molecular vibrations in the so-called vibrational Stark effect. Based on a density functional theory (DFT) approach, here, we report a detailed investigation of the influence of oriented external electric fields (OEEFs) on the dipole moment and infrared (IR) spectrum of the nonpolar centrosymmetric indigo molecule. When an OEEF as intense as ∼0.1 V Å-1 is applied, several modifications in the IR spectrum are observed. Besides the notable frequency shift of some modes, we observe the onset of new bands-forbidden by the selection rules in the zero-field case. Such a neat field-induced modification of the vibrational selection rules, and the subsequent variations of the peaks' intensities in the IR spectrum, paves the way toward the design of smart tools employing centrosymmetric molecules as proxies for mapping local electric fields. In fact, here, we show that the ratio between the IR and the Raman intensities of selected modes is proportional to the square of the local field. This indicator can be used to quantitatively measure local fields, not only in condensed matter systems under standard conditions but also in field-emitting-tip apparatus.

Ab Initio Molecular Dynamics Study of Methanol-Water Mixtures under External Electric Fields.

Intense electric fields applied on H-bonded systems are able to induce molecular dissociations, proton transfers, and complex chemical reactions. Nevertheless, the effects induced in heterogeneous molecular systems such as methanol-water mixtures are still elusive. Here we report on a series of state-of-the-art ab initio molecular dynamics simulations of liquid methanol-water mixtures at different molar ratios exposed to static electric fields. If, on the one hand, the presence of water increases the proton conductivity of methanol-water mixtures, on the other, it hinders the typical enhancement of the chemical reactivity induced by electric fields. In particular, a sudden increase of the protonic conductivity is recorded when the amount of water exceeds that of methanol in the mixtures, suggesting that important structural changes of the H-bond network occur. By contrast, the field-induced multifaceted chemistry leading to the synthesis of e.g., hydrogen, dimethyl ether, formaldehyde, and methane observed in neat methanol, in 75:25, and equimolar methanol-water mixtures, completely disappears in samples containing an excess of water and in pure water. The presence of water strongly inhibits the chemical reactivity of methanol.

Arsenic-nucleotides interactions: an experimental and computational investigation.

Albeit arsenic As(iii) is a well-known carcinogenic contaminant, the modalities by which it interacts with living organisms are still elusive. Details pertaining to the binding properties of As(iii) by common nucleotides such as AMP, ADP and ATP are indeed mostly unknown. Here we present an investigation, conducted via experimental and quantum-based computational approaches, on the stability of the complexes formed by arsenic with those nucleotides. By means of potentiometric and calorimetric measurements, the relative stability of AMP, ADP and ATP has been evaluated as a function of the pH. It turns out that ATP forms more stable structures with As(iii) than ADP which, in turn, better chelates arsenic than AMP. Such a stability sequestration capability of arsenic (ATP > ADP > AMP) has been interpreted on a twofold basis via state-of-the-art ab initio molecular dynamics (AIMD) and metadynamics (MetD) simulations performed on aqueous solutions of As(iii) chelated by AMP and ATP. In fact, we demonstrate that ATP offers a larger number of effective binding sites than AMP, thus indicating a higher statistical probability for chelating arsenic. Moreover, an evaluation of the free energy associated with the interactions that As(iii) establishes with the nucleotide atoms responsible for the binding quantitatively proves the greater effectiveness of ATP as a chelating agent.

Removal of As(III) from Biological Fluids: Mono- versus Dithiolic Ligands.

Arsenic is one of the inorganic pollutants typically found in natural waters, and its toxic effects on the human body are currently of great concern. For this reason, the search for detoxifying agents that can be used in a so-called "chelation therapy" is of primary importance. However, to the aim of finding the thermodynamic behavior of efficient chelating agents, extensive speciation studies, capable of reproducing physiological conditions in terms of pH, temperature, and ionic strength, are in order. Here, we report on the acid-base properties of meso-2,3-dimercaptosuccinic acid (DMSA) at different temperatures (i.e., T = 288.15, 298.15, 310.15, and 318.15 K). In particular, its capability to interact with As(III) has been investigated by experimentally evaluating some crucial thermodynamic parameters (ΔH and TΔS), stability constants, and its speciation model. Additionally, in order to gather information on the microscopic coordination modalities of As(III) with the functional groups of DMSA and, at the same time, to better interpret the experimental results, a series of state-of-the-art ab initio molecular dynamics simulations have been performed. For the sake of completeness, the sequestering capabilities of DMSA-a simple dithiol ligand-toward As(III) are directly compared with those recently emerged from similar analyses reported on monothiol ligands.

Enhanced conductivity of water at the electrified air-water interface: a DFT-MD characterization.

DFT-based molecular dynamics simulations of the electrified air-liquid water interface are presented, where a homogeneous field is applied parallel to the surface plane. We unveil the field intensity for the onset of proton transfer and molecular dissociation; the protonic current/proton conductivity is measured as a function of the field intensity/voltage. The air-water interface is shown to exhibit a proton conductivity twice the one in the liquid water for field intensities below 0.40 V Å-1. We show that this difference arises from the very specific organization of water in the binding interfacial layer (BIL, i.e. the air-water interface region) into a 2D-HBond-network that is maintained and enforced at the electrified interface. Beyond fields of 0.40 V Å-1, water in the BIL and in the bulk liquid are aligned in the same way by the rather intense fields, hence leading to the same proton conductivity in both BIL and bulk water.

Evidence of Structural Inhomogeneities in Hard-Soft Dimeric Particles without Attractive Interactions.

We perform Monte Carlo simulations of a simple hard-soft dimeric model constituted by two tangent spheres experiencing different interactions. Specifically, two hard spheres belonging to different dimers interact via a bare hard-core repulsion, whereas two soft spheres experience a softly repulsive Hertzian interaction. The cross correlations are soft as well. By exploring a wide range of temperatures and densities we investigate the capability of this model to document the existence of structural inhomogeneities indicating the possible onset of aggregates, even if no attraction is set. The fluid phase behavior is studied by analyzing structural and thermodynamical properties of the observed structures, in particular by computing radial distribution functions, structure factors and cluster size distributions. The numerical results are supported by integral equation theories of molecular liquids which allow for a finer and faster spanning of the temperature-density diagram. Our results may serve as a framework for a more systematic investigation of self-assembled structures of functionalized hard-soft dimers able to aggregate in a variety of structures widely oberved in colloidal dispersion.

Monte Carlo simulation and integral equation study of Hertzian spheres in the low-temperature regime.

We investigate the behavior of Hertzian spheres in the fluid phase and in proximity of the freezing threshold by using Monte Carlo (MC) simulations and integral equation theories, based on the Ornstein-Zernike (OZ) approach. The study is motivated by the importance of the Hertzian model in representing a large class of systems interacting via soft interactions, such as star polymers or microgels. Radial distribution functions, structure factors, and excess entropy clearly show the reentrant behavior typical of the Hertzian fluid, well caught by both MC simulations and OZ theory. Then, we make use of some phenomenological one-phase criteria for testing their reliability in detecting the freezing threshold. All criteria provide evidence of the fluid-solid transition with different degrees of accuracy. This suggests the possibility to adopt these empirical rules to provide a quick and reasonable estimate of the freezing transition in model potentials of wide interest for soft matter systems.

Ab initio spectroscopy of water under electric fields.

Whereas a broad range of literature exists on the spectroscopy of water in disparate conditions, infrared (IR) and Raman spectra of water subjected to electric fields have never extensively been investigated so far. Based on ab initio molecular dynamics simulations, here we present IR and Raman spectra of bulk liquid water under the effect of static electric fields. A contraction of the entire frequency range is recorded upon increasing the field intensity both in the IR and in the Raman spectra. Whilst the OH stretching band is progressively shifted toward lower frequencies - indicating a field-induced strengthening of the H-bond network - all the other bands are up-shifted by the field. Furthermore, an evident modification of the librational mode band appears in all the spectra. Finally, the order-maker action of the field emerges also from the increase of the water orientational tetrahedral order. Upon field exposure, the water structure becomes more "ice like".

Interaction between As(III) and Simple Thioacids in Water: An Experimental and ab Initio Molecular Dynamics Investigation.

Albeit arsenic compounds are ubiquitous in aqueous solutions, the speciation of such a pollutant in natural water mainly depends on its binding capabilities with specific molecules. The features of most of the interactions of arsenic complexes can be established in solution, but the data related to the stability of the formed species, essentially depending on the concentration of the ligands, are elusive. For this reason, here, we report on a series of investigations where diverse approaches are combined together in order to characterize the behavior of As(III) species in aqueous solutions where simple chelating agents, such as thiolactic and thiomalic acids, are solvated. By synergistically exploiting potentiometric, calorimetric, and spectroscopic measurements along with ab initio molecular dynamics, the stability and the underlying formation mechanisms of specific species, along with the arsenic coordination modalities with the ligands, have macroscopically and microscopically been assessed. Furthermore, vibrational modes of the complexes formed by arsenic and simple thioacids have been assigned by means of Raman experiments.

Stability of hydrolytic arsenic species in aqueous solutions: As3+vs. As5.

Notwithstanding the fact that arsenic compounds are ubiquitous in the As3+ and As5+ forms in aqueous solutions, most of the microscopic features underlying the conditions of the hydrolysis steps are completely unknown. This way, a first-principles description of the fundamental behaviour of common arsenic species in natural waters and biological fluids is still lacking. Here we report on a synergistic computational and experimental investigation on As3+ and As5+ speciation in aqueous solution under both standard and sizably different alkaline circumstances. If, on the one hand, ab initio molecular dynamics simulations have been used to microscopically trace the different hydrolysis steps of As3+ and As5+ by explicitly taking into account the solvent contribution, on the other hand, they have been able to identify - and predict - the most stable hydrolytic species. In addition, by means of potentiometric and calorimetric measurements, the thermodynamic parameters (log K, ΔH, and TΔS) have been determined at different ionic strength values (0 < I ≤ 1 mol L-1). By comparing the computational and the experimental findings of the species distribution under conditions of some biological fluids, a qualitative agreement on the compounds formed by As3+ and As5+ is thoroughly recorded and, therefore, the stable hydrolytic arsenic species present in natural waters and other biosystems are fully characterised.

SERS and DFT study of indigo adsorbed on silver nanostructured surface.

Surface-enhanced Raman spectroscopy has emerged as a widely used tool in the identification of organic dyes in works of art. Indigo is among the most used organic pigment, its identification can therefore give important information about the provenience and the making of the investigated work of art. In this work, we combine Surface Enhanced Raman Spectroscopy (SERS) experiments with density functional theory (DFT) computations of the Raman frequencies of indigo and an indigo molecule adsorbed onto a silver surface made of 16 silver atoms. The SERS spectrum of a molecule adsorbed on a metallic surface, in fact, can differ from the corresponding Raman one. The knowledge and the comprehension of the SERS spectrum then are mandatory in dyes identification. Experimental SERS spectra were acquired using ad hoc SERS active substrates consisting of pulsed laser ablated silver nanoparticles deposited onto a polishing sheet. The polishing sheet surface roughness is able to remove some pigments grains from the surface of a work of art without damage. DFT calculations provide a good description of the observed SERS spectra, in particular, the indigo-Ag16 structure gives a better description with respect to structures where only one or two silver atoms attached to the indigo molecule are considered.

Mobilities of iodide anions in aqueous solutions for applications in natural dye-sensitized solar cells.

Dye-sensitized solar cells (DSSCs) composed of aqueous electrolytes represent an environmentally friendly, low-cost, and concrete alternative to standard DSSCs and typical solar cells. Although flammable and toxic organic-solvent-based electrolytes have so far been employed more than simpler (iodide) aqueous solutions, recently recorded efficiencies of water-based DSSCs suggest a trend inversion in the near future. Here, we present a study, based on both experiments and ab initio molecular dynamics simulations, in which assessments on the efficiencies of three water electrolytes commonly employed in DSSCs (i.e., LiI, NaI, and KI) are reported. In particular, by atomistically tracing the ability of the iodides as charge carriers and by experimentally measuring the generated currents, we demonstrate that NaI aqueous solutions are more efficient electrolytes than LiI and KI - in descending order - in transporting electrons in DSSCs under bias. Monitoring the role played by the hydration shells of the ionic species under an electric field, we interpret, by first-principles, the various iodide mobilities. This finding, when combined with general considerations on the cation-induced effects on the TiO2 electronic structure, is able to account for the distinct efficiencies of the investigated electrolytes.