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Using quantum mechanical calculations within density functional theory, we provide a comprehensive analysis of infrared-active excitation of water molecules confined in nanocages of a beryl crystal lattice. We calculate infrared-active modes including the translational, librational, and mixed-type resonances of regular and heavy water molecules. The results are compared to the experimental spectra measured for the two principal polarizations of the electric field: parallel and perpendicular to the crystallographic c-axis. Good agreement is achieved between calculated and measured isotopic shifts of the normal modes. We analyze the vibrational modes in connection with the structural characteristics and arrangements of water molecules within the beryl crystal. Specific atomic displacements are assigned to each experimentally detected vibrational mode resolving the properties of nano-confined water on scales not accessible by experiments. Our results elucidate the applicability and efficiency of a combined experimental and computational approach for describing and an in-depth understanding of nano-confined water, and pave the way for future studies of more complex systems. [ABSTRACT FROM AUTHOR]

DNA nucleotides can be interrogated by nanomaterials in order to be detected. With the aid of quantum-mechanical simulations, we unravel the intrinsic details of the electronic transport across nanoelectrodes functionalized with tiny modified diamond-like molecules. These electrodes generate a gap in which DNA nucleotides are placed and can be identified. The identification is strongly affected by the hydrogen bonding characteristics of the diamond-like particle and the nucleotides. The results point to the connection of the electronic transmission across the functionalized nanogap and the electronic and bonding characteristics of the molecular complexes within the nanogap. Specifically, our discussion focuses on the influence of the DNA dynamics on the electronic signals across the nanogap. We identify the molecular complex's details that hinder or promote the electronic transport through an analysis that moves from the bonding within the molecular complex up to the electronic current that this can accommodate. Accordingly, our work discusses pathways for analyzing hydrogen-bonded molecular complexes or molecules hydrogen-bonded to a material part having the optimization of the design of biosensing nanogaps and read-out nanopores in mind. The presented approach, though, is applicable to a wide range of applications utilizing exactly the bio/nano interface., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Room temperature ionic liquid solutions confined between neutral and charged surfaces are investigated by means of atomistic Molecular Dynamics simulations. We study 1-ethyl-3-methylimidazolium dicyanamide ([EMIm] + [DCA] - ) in water or dimethylsulfoxide (DMSO) mixtures in confinement between two interfaces. The analysis is based on the comparison of the molecular species involved and the charged state of the surfaces. Focus is given on the influence of different water/DMSO concentrations on the microstructuring and accumulation of each species. Thermodynamic aspects, such as the entropic contributions in the observed trends are obtained from the simulations using a lattice-gas theory. The results clearly underline the differences in these properties for the water and DMSO mixtures and unravel the underlying mechanisms and inherent details. We were able to pinpoint the importance of the size and the relative permittivity of the molecules in guiding their microstructuring in the vicinity of the surfaces, as well as their interactions with the latter, i.e. the solute-surface interactions. The influence of water and DMSO on the overscreening at charged interfaces is also discussed. The analysis on the molecular accumulation at the interfaces allows us to predict whether the accumulation is entropy or enthalpy driven, which has an impact in the removal of the molecular species from the surfaces. We discuss the impact of this work in providing an essential understanding towards a careful design of electrochemical elements.

A comprehensive understanding of the interactions between organic molecules and a metal oxide surface is essential for an efficient surface modification and the formation of organic-inorganic hybrids with technological applications ranging from heterogeneous catalysis and biomedical templates up to functional nanoporous matrices. In this work, first-principles calculations supported by experiments are used to provide the microstructural characteristics of (101̄0) surfaces of zinc oxide single crystals modified by azide terminated hydrocarbons, which graft on the oxide through a thiol group. On the computational side, we evaluate the specific interactions between the surface and the molecules with the chemical formula N 3 (CH 2 ) n SH, with n = 1, 3, 6, 9. We demonstrate that the molecules chemisorb on the bridge site of ZnO(101̄0). Upon adsorption, the N 3 (CH 2 ) n SH molecules break the neutral (Zn δ + -O δ - ) dimers on ZnO(101̄0) resulting in a structural distortion of the ZnO(101̄0) substrate. The energy decomposition analysis revealed that such structure distortion favors the adsorption of the molecules on the surface leading to a strong correlation between the surface distortion energy and the interaction energy of the molecule. An azide-terminated thiol with three methylene groups in the hydrocarbon chain N 3 (CH 2 ) 3 SH was synthesized, and the assembly of this linker on ZnO surfaces was confirmed through atomic force microscopy. The bonding to the inorganic surface was examined via X-ray photoelectron spectroscopy (XPS). Clear signatures of the organic components on the oxide substrates were observed underlying the successful realization of thiol-grafting on the metal oxide. Temperature-dependent and angle-resolved XPS were applied to examine the thermal stability and to determine the thickness of the grafted SAMs, respectively. We discuss the high potential of our hybrid materials in providing further functionalities towards heterocatalysis and medical applications., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

We study the properties of residual water molecules at different mole fractions in dialkylimidazolium based ionic liquids (ILs), namely 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM/BF 4 ) and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM/BF 4 ) by means of atomistic molecular dynamics (MD) simulations. The corresponding Kirkwood-Buff (KB) integrals for the water-ion and ion-ion correlation behavior are calculated by a direct evaluation of the radial distribution functions. The outcomes are compared to the corresponding KB integrals derived by an inverse approach based on experimental data. Our results reveal a quantitative agreement between both approaches, which paves a way towards a more reliable comparison between simulation and experimental results. The simulation outcomes further highlight that water even at intermediate mole fractions has a negligible influence on the ion distribution in the solution. More detailed analysis on the local/bulk partition coefficients and the partial structure factors reveal that water molecules at low mole fractions mainly remain in the monomeric state. A non-linear increase of higher order water clusters can be found at larger water concentrations. For both ILs, a more pronounced water coordination around the cations when compared to the anions can be observed, which points out that the IL cations are mainly responsible for water pairing mechanisms. Our simulations thus provide detailed insights in the properties of dialkylimidazolium based ILs and their effects on water binding.