Astrochemistry and Astrobiology: Materials Sciencein Wonderland?

Astrochemistry and astrobiology, the fascinating disciplines that strive to unravel the origin of life, have opened unprecedented and unpredicted vistas into exotic compounds as well as extreme or complex reaction conditions of potential relevance for a broad variety of applications. Representative, and so far little explored sources of inspiration include complex organic systems, such as polycyclic aromatic hydrocarbons (PAHs) and their derivatives; hydrogen cyanide (HCN) and formamide (HCONH2) oligomers and polymers, like aminomalononitrile (AMN)-derived species; and exotic processes, such as solid-state photoreactions on mineral surfaces, phosphorylation by minerals, cold ice irradiation and proton bombardment, and thermal transformations in fumaroles. In addition, meteorites and minerals like forsterite, which dominate dust chemistry in the interstellar medium, may open new avenues for the discovery of innovative catalytic processes and unconventional methodologies. The aim of this review was to offer concise and inspiring, rather than comprehensive, examples of astrochemistry-related materials and systems that may be of relevance in areas such as surface functionalization, nanostructures, and hybrid material design, and for innovative technological solutions. The potential of computational methods to predict new properties from spectroscopic data and to assess plausible reaction pathways on both kinetic and thermodynamic grounds has also been highlighted.

Hydration Shell of Antifreeze Proteins: Unveiling the Role of Non-Ice-Binding Surfaces

Antifreeze proteins (AFPs) have the ability to inhibit ice growth by binding to ice nuclei. Their ice-binding mechanism is still unclear, yet the hydration layer is thought to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of two AFPs and two non-AFPs. The calculated shell thickness and density of the AFPs do not feature any relevant difference with respect to the non-AFPs. Moreover, the hydration shell density is always higher than the bulk density and, thus, no low-density, ice-like layer is detected at the ice-binding surface (IBS) of AFPs. Instead, we observe local water-density differences in AFPs between the IBS (lower density) and the non-IBS (higher density). The lower solvent density at the ice-binding site can pave the way to the protein binding to ice nuclei, while the higher solvent density at the non-ice-binding surfaces might provide protection against ice growth.

Potential-Energy Surfaces for Ring-Puckering Motions of Flexible Cyclic Molecules through Cremer-Pople Coordinates: Computation, Analysis, and Fitting

Ring-puckering motion in 12 flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange-correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D_{5 h} or C_{2 v}. The issue of PES fitting and that of solving the nuclear dynamics using ring-puckering coordinates are also addressed. Analytical formulations of the computed PESs using suitable functional forms with a limited set of parameters are provided.

Computational Evidence Suggests That 1-Chloroethanol May Be an Intermediate in the Thermal Decomposition of 2-Chloroethanol into Acetaldehyde and HCl

The dehalogenation of 2-chloroethanol (2ClEtOH) in the gas phase with and without the participation of catalytic water molecules has been investigated using methods rooted into the density functional theory. The well-known HCl elimination leading to vinyl alcohol (VA) was compared to the alternative elimination route toward oxirane and shown to be kinetically and thermodynamically more favorable. However, the isomerization of VA to acetaldehyde in the gas phase, in the absence of water, was shown to be kinetically and thermodynamically less favorable than the recombination of VA and HCl to form the isomeric 1-chloroethanol (1ClEtOH) species. At the ωB97X-D/cc-pVTZ level of calculation, this species is more stable than 2ClEtOH by about 6 kcal mol^-1 at 298 K, and the reaction barrier for VA to 1ClEtOH is 23 kcal mol^-1 versus 55 kcal mol^-1 for the direct transformation of VA to acetaldehyde. In a successive step, 1ClEtOH can decompose directly to acetaldehyde and HCl with a lower barrier (29 kcal mol^-1) than that of VA to the same products (55 kcal mol^-1). The calculations were repeated using a single ancillary water molecule (W) in the complexes 2ClEtOH_W and 1ClEtOH_W. The latter adduct is now more stable than 2ClEtOH_W by about 8 kcal mol^-1 at 298 K, implying that the water molecule increased the already higher stability of 1ClEtOH in the gas phase. However, this catalytic water molecule lowers dramatically the barrier for the interconversion of VA to acetaldehyde (from 55 to 7 kcal mol^-1). This barrier is now smaller than the one for the conversion to 1ClEtOH (which also decreases, but not so much, from 23 to 13 kcal mol^-1). Thus, it is concluded that while 1ClEtOH may be a plausible intermediate in the gas phase dehalogenation of 2ClEtOH, it is unlikely that it plays a major role in water complexes (or, by inference, aqueous solution). It is also shown that neither in the gas phase nor in the cluster with one water molecule, the oxirane path is more favorable than the VA alcohol path. Additionally, a direct conversion of 2ClEtOH to 1ClEtOH through a transition state which resembles a VA molecule in a complex with a chlorine atom and a hydrogen atom on both sides of this planar species was found. This reaction path has also lower activation energy than the conversion to oxirane but not as low as the conversion to VA.

State-of-the-art computation of the rotational and IR spectra of the methyl-cyclopropyl cation: hints on its detection in space

Recent measurements by the Cassini Ion Neutral Mass Spectrometer demonstrated the presence of numerous carbocations in Titan's upper atmosphere. In [Ali et al., Planet. Space Sci., 2013, 87, 96], an analysis of these measurements revealed the formation of the three-membered cyclopropenyl cation and its methyl derivatives. As a starting point of a future coordinated effort of laboratory experiments, quantum-chemical calculations, and astronomical observations, in the present work the molecular structure and spectroscopic properties of the methyl-cyclopropenyl cation have been investigated by means of state-of-the-art computational approaches in order to simulate its rotational and infrared spectra. Rotational parameters have been predicted with an expected accuracy better than 0.1% for rotational constants and on the order of 1-2% for centrifugal-distortion terms. As for the infrared spectrum, despite the challenge of a large amplitude motion, fundamental transitions have been computed to a good accuracy, i.e., the uncertainties are expected to be smaller than 5-10 wavenumbers.

Ferrocenes with simple chiral substituents: an in-depth theoretical and experimental VCD and ECD study

Ferrocenes bearing chiral pendants are investigated through VCD and ECD. The VCD spectra are best interpreted by GVPT2-anharmonic DFT calculations. Diagnostic bands related to the absolute configuration of the title compounds are found in both kinds of spectra.

Two-level stochastic search of low-energy conformers for molecular spectroscopy: implementation and validation of MM and QM models

The search for stationary points in the molecular potential energy surfaces (PES) is a problem of increasing relevance in molecular sciences especially for large, flexible systems featuring several large-amplitude internal motions.

Molecular synthons for accurate structural determinations: the equilibrium geometry of 1-chloro-1-fluoroethene

The equilibrium structure for 1-chloro-1-fluoroethene is obtained by high-level quantum chemical calculations and the semi-experimental approach.

Mechanistic insights into metal ions transit through threefold ferritin channel

BACKGROUND

The mechanism of how the hydrophilic threefold channel (C3) of ferritin nanocages facilitates diffusion of diverse metal ions into the internal cavity remains poorly explored.

METHODS

Computational modeling and free energy estimations were carried out on R. catesbeiana H´ ferritin. Transit features and associated energetics for Fe²⁺, Mg²⁺, Zn²⁺ ions through the C3 channel have been examined.

RESULTS

We highlight that iron conduction requires the involvement of two Fe²⁺ ions in the channel. In such doubly occupied configuration, as observed in X-ray structures, Fe²⁺ is displaced from the internal site (stabilized by D127) at lower energetic cost. Moreover, comparison of Fe²⁺, Mg²⁺ and Zn²⁺ transit features shows that E130 geometric constriction provides not only an electrostatic anchor to the incoming ions but also differentially influence their diffusion kinetics.

CONCLUSIONS

Overall, the study provides insights into Fe²⁺ entry mechanism and characteristic features of metal-protein interactions that influence the metal ions passage. The dynamics data suggest that E130 may act as a metal selectivity gate. This implicates an ion-specific entry mechanism through the channel with the distinct diffusion kinetics being the discriminating factor.

GENERAL SIGNIFICANCE

Ferritin nanocages not only act as biological iron reservoirs but also have gained importance in material science as template scaffolds for synthesizing metal nanoparticles. This study provides mechanistic understanding on the conduction of different metal ions through the channel.

Time-Dependent Formulation of Resonance Raman Optical Activity Spectroscopy

In this work, we extend the theoretical framework recently developed for the simulation of resonance Raman (RR) spectra of medium-to-large sized systems to its chiral counterpart, namely, resonance Raman optical activity (RROA). The theory is based on a time-dependent (TD) formulation, with the transition tensors obtained as half-Fourier transforms of the appropriate cross-correlation functions. The implementation has been kept as general as possible, supporting adiabatic and vertical models for the PES representation, both in Cartesian and internal coordinates, with the possible inclusion of Herzberg-Teller (HT) effects. Thanks to the integration of this TD-RROA procedure within a general-purpose quantum-chemistry program, both solvation and leading anharmonicity effects can be included in an effective way. The implementation is validated on one of the smallest chiral molecule (methyloxirane). Practical applications are illustrated with three medium-size organic molecules (naproxen-OCD₃, quinidine and 2-Br-hexahelicene), whose simulated spectra are compared to the corresponding experimental data.

Unveiling the Sulfur-Sulfur Bridge: Accurate Structural and Energetic Characterization of a Homochalcogen Intermolecular Bond

By combining rotational spectroscopy in supersonic expansion with the capability of state-of-the-art quantum-chemical computations in accurately determining structural and energetic properties, the genuine nature of a sulfur-sulfur chalcogen bond between dimethyl sulfide and sulfur dioxide has been unveiled in a gas-jet environment free from collision, solvent and matrix perturbations. A SAPT analysis pointed out that electrostatic S⋅⋅⋅S interactions play the dominant role in determining the stability of the complex, largely overcoming dispersion and C-H⋅⋅⋅O hydrogen-bond contributions. Indeed, in agreement with the analysis of the quadrupole-coupling constants and of the methyl internal rotation barrier, the NBO and NOCV/CD approaches show a marked charge transfer between the sulfur atoms. Based on the assignment of the rotational spectra for 7 isotopologues, an accurate semi-experimental equilibrium structure for the heavy-atom backbone of the molecular complex has been determined, which is characterized by a S⋅⋅⋅S distance (2.947(3) Å) well below the sum of van der Waals radii.

Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory

Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.

Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite

The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.

An ab initio study of Cu-based delafossites as an alternative to nickel oxide in photocathodes: effects of Mg-doping and surface electronic features

CuMO2 delafossites (M = Al, Ga, and Cr) are p-type semiconductor oxides that have been recently proposed as the electrode in p-type dye-sensitized solar cells (p-DSSC) which is an alternative to the standard, low-performing nickel oxide. To assess this potential application of delafossites, we report here a DFT-based investigation of the structural and electronic properties of CuAlO2, CuGaO2 and CuCrO2. In particular, we address the role of Mg doping to obtain the p-type semiconducting character: the substitution of an M3+ cation with Mg2+ is easier with Ga than with Al and Cr, and, in all cases, the hole introduced by Mg2+ leads to the formation of Cu2+ species. Moreover, we address surface electronic features in order to characterize the most exposed delafossite surface termination and, more importantly, to predict the valence band maximum energy value, which determines the p-DSSC open circuit potential. From analysis of all our results, CuGaO2 emerges as the most promising system that can boost the development of new photocathodes for p-DSSCs.