Structural Characterization of Sulfur-Containing Water Clusters Using a Density-Functional Based Tight-Binding Approach

Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations

Collision-induced dissociation experiments of hydrated molecular species can provide a wealth of important information. However, they often need a theoretical support to extract chemical information. In the present article, in order to provide a detailed description of recent experimental measurements [Braud et al., J. Chem. Phys., 2019, 150, 014303], collision simulations between low-energy protonated uracil water clusters (H₂O)_1-7,11,12UH⁺ and an Ar atom were performed using a quantum mechanics/molecular mechanics formalism based on the self-consistent-charge density-functional based tight-binding method. The theoretical proportion of formed neutral vs. protonated uracil containing clusters, total fragmentation cross sections as well as the mass spectra of charged fragments are consistent with the experimental data which highlights the accuracy of the present simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. We demonstrate that this latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of the time evolution of the fragments populations and of their relative abundances demonstrate that, up to 7 water molecules, a direct dissociation mechanism occurs after collision whereas for 11 and 12 water molecules a statistical mechanism is more likely to participate. Although scarce in the literature, the present simulations appear as a useful tool to complement collision-induced dissociation experiments of hydrated molecular species.

Manifolds of low energy structures for a magic number of hydrated sulfate: SO42-(H2O)24

Low energy structures of SO₄^2-(H₂O)₂₄ have been obtained using a combination of classical molecular dynamics simulations and refinement of structures and energies by quantum chemical calculations. Extensive exploration of the potential energy surface led to a number of low-energy structures, confirmed by accurate calibration calculations. An overall analysis of this large set was made after devising appropriate structural descriptors such as the numbers of cycles and their combinations. Low energy structures bear common motifs, the most prominent being fused cycles involving alternatively four and six water molecules. The latter adopt specific conformations which ensure the appropriate surface curvature to form a closed cage without dangling O-H bonds and at the same time provide 12-coordination of the sulfate ion. A prominent feature to take into account is isomerism via inversion of hydrogen bond orientations along cycles. This generates large families of ca. 100 isomers for this cluster size, spanning energy windows of 10-30 kJ mol^-1. This relatively ignored isomerism must be taken into account to identify reliably the lowest energy minima. The overall picture is that the magic number cluster SO₄^2-(H₂O)₂₄ does not correspond to formation of a single, remarkable structure, but rather to a manifold of structural families with similar stabilities. Extensive calculations on isomerization mechanisms within a family indicate that large barriers are associated to direct inversion of hydrogen bond networks. Possible implications of these results for magic number clusters of other anions are discussed.

Simulation of Liquids with the Tight-Binding Density-Functional Approach and Improved Atomic Charges

Theoretical description of liquids, especially liquid water, is an ongoing subject with important implications in various domains such as homogeneous catalysis; solvation of molecular, ionic, and biomolecular species; and reactivity. Various formalisms exist to describe liquids, each one displaying its own balance between accuracy and computational cost that defines its range of applications. The present article revisits the ability of the density-functional-based tight-binding (SCC-DFTB) approach to model liquids by focusing on liquid water and liquid benzene under ambient conditions. To do so, we benchmark a recent correction for the SCC-DFTB atomic charges that allows for a drastic improvement of the pair radial distribution functions of liquid water as compared to both experimental data and density-functional theory results performed in the generalized-gradient approximation. We also report the coupling of the deMonNano and i-PI codes to perform path-integral molecular dynamics. This allows us to rationalize the impact of nuclear quantum effects on the SCC-DFTB description of liquid water. This study evidences the rather good ability of SCC-DFTB to describe liquid water and liquid benzene. As the first example of application, we also present results for a benzene molecule solvated in water with the perspectives of further studies devoted to solvent/water interfaces.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

Density-functional tight-binding approach for metal clusters, nanoparticles, surfaces and bulk: application to silver and gold

Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic and hybrid materials. The present topical review addresses the ability and performance of DFTB to investigate energetic, structural, spectroscopic and dynamical properties of gold and silver materials. After a brief overview of the theoretical basis of DFTB, its parametrization and its transferability, we report its past and recent applications to gold and silver systems, including small clusters, nanoparticles, bulk and surfaces, bare and interacting with various organic and inorganic compounds. The range of applications covered by those studies goes from plasmonics and molecular electronics, to energy conversion and surface chemistry. Finally, perspectives of DFTB in the field of gold and silver surfaces and NPs are outlined.

Theoretical determination of adsorption and ionisation energies of polycyclic aromatic hydrocarbons on water ice

In dense interstellar environments, Polycyclic Aromatic Hydrocarbons (PAHs) are likely to condense onto or integrate into water ice mantles covering dust grains. Understanding the role of ice in the photo-induced processes involving adsorbed PAHs is therefore a key issue in astrochemistry. This requires (i) the knowledge of PAH-ice interactions, i.e. PAH-ice adsorption energies and local structures at the PAH-ice interface, as well as (ii) the understanding of the fate of electrons in the PAH-ice system upon excitation. Regarding (i), in this work, we determined the lowest energy structures of PAH-ice systems for a variety of PAHs ranging from naphthalene to ovalene on three types of ice - crystalline (Ih and Ic) and amorphous (low density) - using an explicit description of the electrons and a finite-sized system. The electronic structure was determined using the Self Consistent Charge Density Functional based Tight Binding (SCC-DFTB) scheme with modified Mulliken charges in order to ensure a good description of the studied systems. Regarding (ii), the influence of the interaction with ice on the Vertical Ionisation Potentials (VIPs) of the series of PAHs was determined using the constrained SCC-DFTB scheme benchmarked against correlated wavefunction results for PAH-(H₂O)_n (n = 1-6, 13) clusters. The results show a deviation equal, at most, to ∼1.4 eV of the VIPs of PAHs adsorbed on ice with respect to the gas phase values. Our results are discussed in the light of experimental data and previous theoretical studies.

Theoretical investigation of the solid–liquid phase transition in protonated water clusters

Molecular dynamics simulations provide an atomistic scale description of the phase transition in protonated water clusters (H₂O)_nH⁺(n= 20–23) and an interpretation to recent nano-calorimetric experiments.