Unraveling the coherent dynamic structure factor of liquid water at the mesoscale by molecular dynamics simulations

Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments

Molecular Dynamics simulations study material structure and dynamics at the atomic level. X-ray and neutron scattering experiments probe exactly the same time- and length scales as the simulations. In order to benchmark simulations against measured scattering data, a program is required that computes scattering patterns from simulations with good single-core performance and support for parallelization. In this work, the existing program Sassena is used as a potent solution to this requirement for a range of scattering methods, covering pico- to nanosecond dynamics, as well as the structure from some Ångströms to hundreds of nanometers. In the case of nanometer-level structures, the finite size of the simulation box, which is referred to as the finite size effect, has to be factored into the computations for which a method is described and implemented into Sassena. Additionally, the single-core and parallelization performance of Sassena is investigated, and several improvements are introduced.

On De Gennes narrowing of fluids confined at the molecular scale in nanoporous materials

Beyond well-documented confinement and surface effects arising from the large internal surface and severely confining porosity of nanoporous hosts, the transport of nanoconfined fluids remains puzzling in many aspects. With striking examples such as memory, i.e., non-viscous effects, intermittent dynamics, and surface barriers, the dynamics of fluids in nanoconfinement challenge classical formalisms (e.g., random walk, viscous/advective transport)-especially for molecular pore sizes. In this context, while molecular frameworks such as intermittent Brownian motion, free volume theory, and surface diffusion are available to describe the self-diffusion of a molecularly confined fluid, a microscopic theory for collective diffusion (i.e., permeability), which characterizes the flow induced by a thermodynamic gradient, is lacking. Here, to fill this knowledge gap, we invoke the concept of "De Gennes narrowing," which relates the wavevector-dependent collective diffusivity D0(q) to the fluid structure factor S(q). First, using molecular simulation for a simple yet representative fluid confined in a prototypical solid (zeolite), we unravel an essential coupling between the wavevector-dependent collective diffusivity and the structural ordering imposed on the fluid by the crystalline nanoporous host. Second, despite this complex interplay with marked Bragg peaks in the fluid structure, the fluid collective dynamics is shown to be accurately described through De Gennes narrowing. Moreover, in contrast to the bulk fluid, the departure from De Gennes narrowing for the confined fluid in the macroscopic limit remains small as the fluid/solid interactions in severe confinement screen collective effects and, hence, weaken the wavevector dependence of collective transport.

The Debye's model for the dielectric relaxation of liquid water and the role of cross-dipolar correlations. A MD-simulations study

By means of massive (more than 1.2 · 106 molecules) molecular dynamics simulations at 300 K we have disentangled self- and cross-dipolar contributions to the dielectric relaxation of liquid water that cannot be experimentally resolved. We have demonstrated that cross dipolar correlations are of paramount importance. They amount for almost a 60% of the total dielectric amplitude. The corresponding relaxation function is a one-step Debye-like function with a characteristic time, τcross, of the order of the phenomenological Debye time, τD. In contrast, the relaxation function corresponding to the self-contribution is rather complex and contains a fast decay related to dipolar librations and a second relaxation step that can be well described by two exponentials: a low-amplitude fast process (τ0 = 0.31 ps) and a main slow process (τself = 5.4 ps) that fully randomizes the dipolar orientation. In addition to dipolar relaxation functions, we have also calculated scattering-like magnitudes characterizing translation and rotation of water molecules. Although these processes can be considered as "jump" processes in the short time range, at the time scale of about τD-τcross, at which the cross-dipolar correlations decay to zero, the observed behavior cannot be distinguished from that corresponding to uncoupled Brownian translational and rotational diffusion. We propose that this is the reason why the Debye model, which does not consider intermolecular dipolar interactions, seems to work at time t ≳ τD.

Neutron scattering studies on dynamics of lipid membranes

Neutron scattering methods are powerful tools for the study of the structure and dynamics of lipid bilayers in length scales from sub Å to tens to hundreds nm and the time scales from sub ps to μs. These techniques also are nondestructive and, perhaps most importantly, require no additives to label samples. Because the neutron scattering intensities are very different for hydrogen- and deuterium-containing molecules, one can replace the hydrogen atoms in a molecule with deuterium to prepare on demand neutron scattering contrast without significantly altering the physical properties of the samples. Moreover, recent advances in neutron scattering techniques, membrane dynamics theories, analysis tools, and sample preparation technologies allow researchers to study various aspects of lipid bilayer dynamics. In this review, we focus on the dynamics of individual lipids and collective membrane dynamics as well as the dynamics of hydration water.

Collective dynamics and self-motions in the van der Waals liquid tetrahydrofuran from meso- to inter-molecular scales disentangled by neutron spectroscopy with polarization analysis

By using time-of-flight neutron spectroscopy with polarization analysis, we have separated coherent and incoherent contributions to the scattering of deuterated tetrahydrofuran in a wide scattering vector (Q)-range from meso- to inter-molecular length scales. The results are compared with those recently reported for water to address the influence of the nature of inter-molecular interactions (van der Waals vs hydrogen bond) on the dynamics. The phenomenology found is qualitatively similar in both systems. Both collective and self-scattering functions are satisfactorily described in terms of a convolution model that considers vibrations, diffusion, and a Q-independent mode. We observe a crossover in the structural relaxation from being dominated by the Q-independent mode at the mesoscale to being dominated by diffusion at inter-molecular length scales. The characteristic time of the Q-independent mode is the same for collective and self-motions and, contrary to water, faster and with a lower activation energy (≈1.4 Kcal/mol) than the structural relaxation time at inter-molecular length scales. This follows the macroscopic viscosity behavior. The collective diffusive time is well described by the de Gennes narrowing relation proposed for simple monoatomic liquids in a wide Q-range entering the intermediate length scales, in contraposition to the case of water.

Understanding the coherent dynamic structure factor of liquid water measured by neutron spectroscopy with polarization analysis: a Molecular Dynamics simulations study

This work is focused on atomistic molecular dynamics (MD) simulations of water carried out at 300 K. The main goal is to better understand the experimental results of the coherent dynamic structure factor S(Q,ν) of D2O that were obtained by means of neutron scattering with polarization analysis and previously reported by us [A. Arbe et al. Phys. Rev. Res. 2, 022015 (2020)]. From the simulations, we have calculated the coherent dynamic structure factor in the time domain S(Q,t) as well as its selfand distinctcontributions. We have also calculated S(Q,t) corresponding to a H2O sample. The main results obtained are: (i) The Q-independent relaxation process identified in S(Q,ν) in the mesoscopic range (Q0-mode) is the responsible of the restructuring of the hydrogen bond (HB) network at times shorter than that corresponding to the molecular diffusion; (ii) the vibrational contribution identified at high frequency in S(Q,ν) corresponds to a hydrodynamic-like mode propagating in an elastic medium (fixed HB bonding pattern); (iii) in the crossover range from mesoscopic to intermolecular scales, diffusion also progressively contributes to the decay of density fluctuations; (iv) MD-simulations suggest that it would be basically impossible to measure S(Q,ν,) of H2O in the mesoscopic range with the current neutron scattering capabilities.

Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments

The atomistic structure and dynamics obtained from molecular dynamics (MD) simulations with the example of TIP3P (rigid and flexible) and TIP4P/2005 (rigid) water is compared to neutron and X-ray scattering data at ambient conditions. Neutron and X-ray diffractograms are calculated from the simulations for four isotopic substitutions as well as the incoherent intermediate scattering function for neutrons. The resulting curves are compared to each other and to published experimental data. Differences between simulated and measured intermediate scattering functions are quantified by fitting an analytic model to the computed values. The sensitivity of the scattering curves to the parameters of the MD simulations is demonstrated on the example of two parameters, bond length and angle.