Christoph Allolio

An Ab Initio Microscope: Molecular Contributions to the Femtosecond Time-Dependent Fluorescence Shift of a Reichardt-Type Dye†

The molecular probe N-methyl-6-quinolone (MQ) gives spectroscopic access to its local environment.[1] Its experimentally observed time-dependent Stokes shift can be explained by molecular dynamics simulations in combination with DFT calculations. Decomposition of the MD trajectories shows that an important contribution to the time-dependent Stokes shift originates from a group of water molecules that strongly interact with the molecular dipole of MQ.[2]

H-bonding competition and clustering in aqueous LiI.

We have characterized the structure and picosecond dynamics of the hydrogen bond network of solvated LiI by means of first-principles molecular dynamics simulations at ambient temperature. Our calculations reveal the qualitative differences of the network between low (1 M) and high (9 M) salt concentrations. In particular, we find the presence of fused Li(+) solvation shells at 9 M, meaning that a single water molecule is coordinated to two different Li(+) ions. This results in the formation of (Li(+)·H2O)n chains, dominating over conventional ion pairing. We report experimental and simulated NMR chemical shifts, which indicate a weakening of the hydrogen bond network, mainly within the first solvation shell of the I(-) ions. In line with this finding, the local dynamics of this network reveal a competition between the chaotropic effects of I(-) and the kosmotropic properties of Li(+) ions at an intermediate range. We find that the chaotropic effect of I(-) reaches across several H-bonds into the solution, whereas the kosmotropic effect of Li(+) is more short ranged.

First Principles Calculations of NMR Chemical Shifts of Liquid Water at an Amorphous Silica Interface

Abstract We investigate the anomalous structure and hydrogen bond network of water molecules confined inside a silica nanopore (MCM-41 type). In addition to geometric data, we use proton NMR chemical shifts as a measure for the strength of the H-bonding network. We compute the 1H NMR shifts of confined water based on a first principle approach in the framework of density functional perturbation theory under periodic boundary conditions. The hydrophilic character of the silica is well manifested in the water density profile. Our calculations illustrate both the modifications of the 1H NMR chemical shifts of the water with respect to bulk water and a considerable slowing down of water diffusion. In the vicinity of silanols, weakly hydrogen bonded liquid water is observed, while at the center region of the pore, the hydrogen bonding network is enhanced with respect to bulk water.

Ab Initio H2O in Realistic Hydrophilic Confinement

A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long-range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized.

Guanidinium Pairing Facilitates Membrane Translocation

Ab initio free energy calculations of guanidinium pairing in aqueous solution confirm the counterintuitive conjecture that the like-charge ion pair is thermodynamically stable. Transferring the guanidinium pair to the inside of a POPC lipid bilayer, like-charge ion pairing is found to occur also inside the membrane defect. It is found to contribute to the nonadditivity of ion transfer, thereby facilitating the presence of ions inside the bilayer. The effect is quantified by free energy decomposition and comparison with ammonium ions, which do not form a stable pair. The presence of two charges inside the center of the bilayer leads to the formation of a pore. Potential consequences for cell penetrating peptides and ion conduction are drawn.

Water Wires in Aqueous Solutions from First-Principles Calculations

We elucidate the concept of water wires in aqueous solutions in view of their structural and dynamical properties by means of first-principles molecular dynamics simulations. We employ a specific set of hydroxyquinoline derivatives (heteroaromatic fluorescent dyes) as probe molecules that provide a well-defined initial and final coordinate for possible water wires by means of their photoacid and photobase functionalities. Besides the geometric structure of the hydrogen bond network connecting these functional sites, we focus on the dependence of the length of the resulting water wire on the initial/final coordinates determined by the chromophore. Special attention is devoted to the persistence of the wires on the picosecond time scale and their capability of shifting the nature of the proton transfer process from a concerted to a stepwise mechanism. Our results shed light on the long debate on whether water wires represent characteristic structural motifs or transient phenomena.

Increased Binding of Calcium Ions at Positively Curved Phospholipid Membranes

Calcium ion is the ubiquitous messenger in cells and plays a key role in neuronal signaling and fusion of synaptic vesicles. These vesicles are typically ∼20-50 nm in diameter, and thus their interaction with calcium ions cannot be modeled faithfully with a conventional flat membrane bilayer setup. Within our newly developed molecular dynamics simulations setup, we characterize here interactions of the calcium ion with curved membrane interfaces with atomistic detail. The present molecular dynamics simulations together with time-dependent fluorescence shift experiments suggest that the mode and strength of interaction of calcium ion with a phospholipid bilayer depends on its curvature. Potential of mean force calculations demonstrate that the binding of calcium ion to the positively curved side of the bilayer is significantly stronger compared with that to a flat membrane.

Orientation-Induced Adsorption of Hydrated Protons at the Air–Water Interface

The surface tension of the air-water interface increases upon addition of inorganic salts, implying a negative surface excess of ionic species. Most acids, however, induce a decrease in surface tension, indicating a positive surface excess of hydrated protons. In combination with the apparent negative charge at pure air-water interfaces derived from electrokinetic experiments, this experimental observation has been a source of intense debate since the mid-19th century. Herein, we calculate surface tensions and ionic surface propensities at air-water interfaces from classical, thermodynamically consistent molecular dynamics simulations. The surface tensions of NaOH, HCl, and NaCl solutions show outstanding quantitative agreement with experiment. Of the studied ions, only H3 O+ adsorbs to the air-water interface. The adsorption is explained by the deep potential well caused by the orientation of the H3 O+ dipole in the interfacial electric field, which is confirmed by ab initio simulations.

Dynamical Dimension to the Hofmeister Series: Insights from First‐Principles Simulations

A systematic characterization of the competing kosmotropic and chaotropic effects of a series of divalent salts on the aqueous H-bonding structure by means of first-principles molecular dynamics simulations is presented. The structural properties are quantified by means of experimental and computed (1) H NMR chemical shifts, whereby the local environments of cations and anions can be discriminated. Complementary to the well-established structural features, a dynamical aspect is added to the concept of kosmotropes and chaotropes. The H-bond dynamics, quantified in terms of the H-bonding autocorrelation functions, shows a good correlation with the structural kosmotropic and chaotropic modifications, which are commonly referred to as the Hofmeister series. The considerably enhanced (reduced) fluctuations of the H-bonding network in the hydration shells around the anions (cations) are a complementary dynamical dimension to the concept of kosmotropic/chaotropic behavior of solvated ions.