Structure and Dynamics of ATP and the ATP-Zn Complex in Solution.

Despite the crucial role of ATP in life and artificial life-like applications, fundamental aspects relevant to its function, such as its conformational properties and its interaction with water and ions, remain unclear. Here, by integrating linear and two-dimensional infrared spectroscopy with molecular dynamics, we provide a detailed characterization of the vibrational spectra of the phosphate groups in ATP and in its complex with Zn in water. Our study highlights the role of conformational disorder and solvation dynamics, beyond the harmonic normal-mode analysis, and reveals a complex scenario in which electronic and environmental effects tune the coupling between phosphate vibrations.

Differential Capacitance of Ionic Liquid Confined between Metallic Interfaces.

We present here a detailed analysis of the electric double layer at the gold electrode/[BMIM][BF] interface using a polarizable model for the electrode, based on our recent approach to include image charges [Geada et al. 716]. A double bell (camel) shape is obtained for the differential capacitance, where the inclusion of metal polarization allows for a higher density of ions in the double layer, particularly around the maxima, thereby increasing the capacitance.

Molecular dynamics simulations of electrified interfaces including the metal polarisation.

Understanding electrified interfaces requires an accurate description of the electric double layer which also takes into account the metal polarisation. Here we present a simple approach to the molecular dynamics simulation of electrified interfaces which combines fixed charges and a core-shell model for the description of the polarisable electron density on the metal electrode. The approach has been applied to the Au(111) surface in contact with a NaCl aqueous electrolyte solution in order to calculate the differential capacitance and to gain a detailed picture of the charging mechanism.

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment.

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems.

Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly.

Following nature's example, there is currently strong interest in using adenosine 5'-triphosphate (ATP) as a fuel for the self-assembly of functional materials with transient/non-equilibrium behaviours. These hold great promise for applications, in catalysis and drug delivery. In a recent seminal work [Maiti , , 2016, , 725], binding of ATP to the metallosurfactant zinc hexadecyl-1,4,7-triazacyclononane ([ZnC TACN]) was exploited to produce ATP-fueled transient vesicles.

Charging of Dielectric Surfaces in Contact with Aqueous Electrolytes─the Influence of CO.

The charge state of dielectric surfaces in aqueous environments is of fundamental and technological importance. Here, we study the influence of dissolved molecular CO on the charging of three chemically different surfaces (SiO, Polystyrene, Perfluorooctadecyltrichlorosilane). We determine their charge state from electrokinetic experiments.

Lower degree of dissociation of pyruvic acid at water surfaces than in bulk.

Understanding the acid/base behavior of environmentally relevant organic acids is of key relevance for accurate climate modelling. Here we investigate the effect of pH on the (de)protonation state of pyruvic acid at the air-water interface and in bulk by using the analytical techniques surface-specific vibrational sum frequency generation and attenuated total reflection spectroscopy. To provide a molecular interpretation of the observed behavior, simulations are carried out using a free energy perturbation approach in combination with electronic structure-based molecular dynamics.

Effects of shear flow on the structure and dynamics of ionic liquids in a metallic nanoconfinement.

It has been shown that a weak shear can induce crystallisation in a disordered, glassy state. In this study, we use molecular dynamics simulations in order to investigate the out-of-equilibrium properties of [BMIM][BF] confined between metal slabs. In particular, we want to understand the extent to which the shear flow modifies the interfacial properties.

On the origin of controlled anisotropic growth of monodisperse gold nanobipyramids.

We elucidate the crucial role of the cetyl trimethylammonium bromide (CTAB) surfactant in the anisotropic growth mechanism of gold nano-bipyramids, nano-objects with remarkable optical properties and high tunability. Atomistic molecular dynamics simulations predict different surface coverages of the CTAB (positively charged) heads and their (bromide) counterions as function of the gold exposed surfaces. High concentration of CTAB surfactant promotes formation of gold nanograins in solution that work as precursors for the smooth anisotropic growth of more elongated nano-bipyramidal objects.

Role of pH in the synthesis and growth of gold nanoparticles using L-asparagine: a combined experimental and simulation study.

The use of biomolecules as capping and reducing agents in the synthesis of metallic nanoparticles constitutes a promising framework to achieve desired functional properties with minimal toxicity. The system's complexity and the large number of variables involved represent a challenge for theoretical and experimental investigations aiming at devising precise synthesis protocols. In this work, we use L-asparagine (Asn), an amino acid building block of large biomolecular systems, to synthesise gold nanoparticles (AuNPs) in aqueous solution at controlled pH.

Surface Charges at the CaF /Water Interface Allow Very Fast Intermolecular Vibrational-Energy Transfer.

We investigate the dynamics of water in contact with solid calcium fluoride, where at low pH, localized charges can develop upon fluorite dissolution. We use 2D surface-specific vibrational spectroscopy to quantify the heterogeneity of the interfacial water (D O) molecules and provide information about the sub-picosecond vibrational-energy-relaxation dynamics at the buried solid/liquid interface. We find that strongly H-bonded OD groups, with a vibrational frequency below 2500 cm , display very rapid spectral diffusion and vibrational relaxation; for weakly H-bonded OD groups, above 2500 cm , the dynamics slows down substantially.

Role of image charges in ionic liquid confined between metallic interfaces.

The peculiar properties of ionic liquids in confinement have not only become essential for energy storage, catalysis and tribology, but still pose fundamental questions. Recently, an anomalous liquid-solid phase transition has been observed in atomic force microscopy experiments for 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF]), the transition being more pronounced for metallic surfaces. Image charges have been suggested as the key element driving the anomalous freezing.

The puzzling issue of silica toxicity: are silanols bridging the gaps between surface states and pathogenicity?

Background: Silica continues to represent an intriguing topic of fundamental and applied research across various scientific fields, from geology to physics, chemistry, cell biology, and particle toxicology. The pathogenic activity of silica is variable, depending on the physico-chemical features of the particles. In the last 50 years, crystallinity and capacity to generate free radicals have been recognized as relevant features for silica toxicity.

Heterogeneous Interactions between Gas-Phase Pyruvic Acid and Hydroxylated Silica Surfaces: A Combined Experimental and Theoretical Study.

The adsorption of gas-phase pyruvic acid (CHCOCOOH) on hydroxylated silica particles has been investigated at 296 K using transmission Fourier transform infrared (FTIR) spectroscopy and theoretical simulations. Under dry conditions (<1% relative humidity, RH), both the trans-cis (Tc) and trans-trans (Tt) pyruvic acid conformers are observed on the surface as well as the (hydrogen bonded) pyruvic acid dimer. The detailed surface interactions were further understood through ab initio molecular dynamics simulations.

Dynamical heterogeneities of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations.

Room temperature ionic liquids (RTILs) have been shown to exhibit spatial heterogeneity or structural heterogeneity in the sense that they form hydrophobic and ionic domains. Yet studies of the relationship between this structural heterogeneity and the ∼picosecond motion of the molecular constituents remain limited. In order to obtain insight into the time scales relevant to this structural heterogeneity, we perform molecular dynamics simulations of a series of RTILs.

A set-up for simultaneous measurement of second harmonic generation and streaming potential and some test applications.

We present a measurement cell that allows simultaneous measurement of second harmonic generation (SHG) and streaming potential (SP) at mineral-water interfaces with flat specimen that are suitable for non-linear optical (NLO) studies. The set-up directly yields SHG data for the interface of interest and can also be used to obtain information concerning the influence of flow on NLO signals from that interface. The streaming potential is at present measured against a reference substrate (PTFE).

Atypical titration curves for GaAl Keggin-ions explained by a joint experimental and simulation approach.

Although they have been widely used as models for oxide surfaces, the deprotonation behaviors of the Keggin-ions (MeAl) and typical oxide surfaces are very different. On Keggin-ions, the deprotonation occurs over a very narrow pH range at odds with the broad charging curve of larger oxide surfaces. Depending on the Me concentration, the deprotonation curve levels off sooner (high Me concentration) or later (for low Me concentration).

A Microscopic Interpretation of Pump-Probe Vibrational Spectroscopy Using Ab Initio Molecular Dynamics.

What happens when extra vibrational energy is added to water? Using nonequilibrium molecular dynamics simulations, also including the full electronic structure, and novel descriptors, based on projected vibrational density of states, we are able to follow the flow of excess vibrational energy from the excited stretching and bending modes. We find that the energy relaxation, mostly mediated by a stretching-stretching coupling in the first solvation shell, is highly heterogeneous and strongly depends on the local environment, where a strong hydrogen bond network can transport energy with a time scale of 200 fs, whereas a weaker network can slow down the transport by a factor 2-3.

Increased Acid Dissociation at the Quartz/Water Interface.

As shown by a quite significant amount of literature, acids at the water surface tend to be "less" acid, meaning that their associated form is favored over the conjugated base. What happens at the solid/liquid interface? In the case of the silica/water interface, we show how the acidity of adsorbed molecules can instead increase. Using a free energy perturbation approach in combination with electronic structure-based molecular dynamics simulations, we show how the acidity of pyruvic acid at the quartz/water interface is increased by almost two units.

Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential.

Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom.

Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles.

Nanophase segregation of a bicomponent thiol self-assembled monolayer is predicted using atomistic molecular dynamics simulations and experimentally confirmed. The simulations suggest the formation of domains rich in acid-terminated chains, on one hand, and of domains rich in amide-functionalized ethylene glycol oligomers, on the other hand. In particular, within the amide-ethylene glycol oligomers region, a key role is played by the formation of interchain hydrogen bonds.

Sum Frequency Generation Spectra from Velocity-Velocity Correlation Functions.

We developed an expression for the calculation of the sum frequency generation spectra (SFG) of water interfaces that is based on the projection of the atomic velocities on the local normal modes. Our approach permits one to obtain the SFG signal from suitable velocity-velocity correlation functions, reducing the computational cost to that of the accumulation of a molecular dynamics trajectory, and therefore cutting the overhead costs associated with the explicit calculation of the dipole moment and polarizability tensor. Our method permits to interpret the peaks in the spectrum in terms of local modes, also including the bending region.

From Gold Nanoseeds to Nanorods: The Microscopic Origin of the Anisotropic Growth.

Directly manipulating and controlling the size and shape of metal nanoparticles is a key step for their tailored applications. In this work, molecular dynamics simulations were applied to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. Different factors influencing the growth were selectively included in the models to unravel the role of the surfactants and ions.

pKa at Quartz/Electrolyte Interfaces.

Acidity of silanol sites at the crystalline quartz/aqueous electrolyte (NaCl, NaI, KCl) interfaces are calculated from ab initio molecular dynamics simulations. pKa's are found to follow a combination of the cationic and anionic Hofmeister series in the order pKa(neat solution) < pKa(NaCl) < pKa(NaI) < pKa(KCl), in agreement with experimental measurements. Rationalization of this ranking is achieved in terms of the microscopic local solvation of the protonated silanols and their conjugated bases, the silanolates SiO(-).