Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dielectric Properties of Nanoconfined Water from Ab Initio Thermopotentiostat Molecular Dynamics.

ABSTRACT: We discuss how to include our recently proposed thermopotentiostat technique [Deissenbeck et al. Phys. Rev. Lett. 2021, 126, 136803] into any existing ab initio molecular dynamics (AIMD) package. Using thermopotentiostat AIMD simulations in the canonical NVTΦ ensemble at a constant electrode potential, we compute the polarization bound charge and dielectric response of interfacial water from first principles.

SUBMITTER: Deißenbeck F

PROVIDER: S-EPMC9933428 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Dielectric Properties of Nanoconfined Water from Ab Initio Thermopotentiostat Molecular Dynamics.

Deißenbeck Florian F Wippermann Stefan S

Journal of chemical theory and computation 20230127 3

We discuss how to include our recently proposed thermopotentiostat technique [Deissenbeck et al. Phys. Rev. Lett. 2021, 126, 136803] into any existing ab initio molecular dynamics (AIMD) package. Using thermopotentiostat AIMD simulations in the canonical NVTΦ ensemble at a constant electrode potential, we compute the polarization bound charge and dielectric response of interfacial water from first principles. ...[more]

PMID: 36705611

Similar Datasets

Ab Initio Molecular Dynamics Simulation of Water Transport through Short Carbon Nanotubes

Project description:Water transport through short single-walled (6, 6) carbon

| S-EPMC9647839 | biostudies-literature

Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations.

Project description:The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.

| S-EPMC4600984 | biostudies-literature

An ab-initio computational method to determine dielectric properties of biological materials.

Project description:Frequency dependent dielectric properties are important for understanding the structure and dynamics of biological materials. These properties can be used to study underlying biological processes such as changes in the concentration of biological materials, and the formation of chemical species. Computer simulations can be used to determine dielectric properties and atomic details inaccessible via experimental methods. In this paper, a unified theory utilizing molecular dynamics and density functional theory is presented that is able to determine the frequency dependent dielectric properties of biological materials in an aqueous solution from their molecular structure alone. The proposed method, which uses reaction field approximations, does not require a prior knowledge of the static dielectric constant of the material. The dielectric properties obtained from our method agree well with experimental values presented in the literature.

| S-EPMC3667492 | biostudies-literature

Probing the self-ionization of liquid water with ab initio deep potential molecular dynamics.

Project description:The chemical equilibrium between self-ionized and molecular water dictates the acid-base chemistry in aqueous solutions, yet understanding the microscopic mechanisms of water self-ionization remains experimentally and computationally challenging. Herein, Density Functional Theory (DFT)-based deep neural network (DNN) potentials are combined with enhanced sampling techniques and a global acid-base collective variable to perform extensive atomistic simulations of water self-ionization for model systems of increasing size. The explicit inclusion of long-range electrostatic interactions in the DNN potential is found to be crucial to accurately reproduce the DFT free energy profile of solvated water ion pairs in small (64 and 128 H2O) cells. The reversible work to separate the hydroxide and hydronium to a distance [Formula: see text] is found to converge for simulation cells containing more than 500 H2O, and a distance of [Formula: see text] 8 Å is the threshold beyond which the work to further separate the two ions becomes approximately zero. The slow convergence of the potential of mean force with system size is related to a restructuring of water and an increase of the local order around the water ions. Calculation of the dissociation equilibrium constant illustrates the key role of long-range electrostatics and entropic effects in the water autoionization process.

| S-EPMC10655216 | biostudies-literature

Hydrogen-Bond Structure and Low-Frequency Dynamics of Electrolyte Solutions: Hydration Numbers from ab Initio Water Reorientation Dynamics and Dielectric Relaxation Spectroscopy.

Project description:We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk-like behavior. The application of this computational protocol to magnesium chloride (MgCl2 ) solutions at different concentrations (0.6-2.8 mol kg-1 ) gives h values in excellent agreement with experimental hydration numbers obtained using GHz-to-THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well-defined criterion for the definition of hydration number and provides a link with the molecular-level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water-water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl2 has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg-water interaction rather than the Cl-water interaction.

| S-EPMC7702081 | biostudies-literature

Modeling Electrified Pt(111)-Had/Water Interfaces from Ab Initio Molecular Dynamics.

Project description:Unraveling the atomistic structures of electric double layers (EDL) at electrified interfaces is of paramount importance for understanding the mechanisms of electrocatalytic reactions and rationally designing electrode materials with better performance. Despite numerous efforts dedicated in the past, a molecular level understanding of the EDL is still lacking. Combining the state-of-the-art ab initio molecular dynamics (AIMD) and recently developed computational standard hydrogen electrode (cSHE) method, it is possible to realistically simulate the EDL under well-defined electrochemical conditions. In this work, we report extensive AIMD calculation of the electrified Pt(111)-Had/water interfaces at the saturation coverage of adsorbed hydrogen (Had) corresponding to the typical hydrogen evolution reaction conditions. We calculate the electrode potentials of a series of EDL models with various surface charge densities using the cSHE method and further obtain the Helmholtz capacitance that agrees with experiment. Furthermore, the AIMD simulations allow for detailed structural analyses of the electrified interfaces, such as the distribution of adsorbate Had and the structures of interface water and counterions, which can in turn explain the computed dielectric property of interface water. Our calculation provides valuable molecular insight into the electrified interfaces and a solid basis for understanding a variety of electrochemical processes occurring inside the EDL.

| S-EPMC8395682 | biostudies-literature

Water-air interface revisited by means of path-integral ab initio molecular dynamics.

Project description:Although nuclear quantum effects (NQEs) have been considered on bulk liquid water, the impact of these latter on the air-water interface has not yet been reported. Herein, by performing and comparing ab initio molecular dynamics (AIMD) and path integral AIMD (PI-AIMD) simulations, we reveal the impact of NQEs on structural, dynamical and electronic properties as well as IR spectra of the air-water interface at room temperature. NQEs, being able to describe a more accurate proton delocalization in H-bonded system than AIMD, reveal a different structural arrangement and dynamical behaviour of both bulk and interfacial water molecules in comparison to AIMD results. A more de-structured and de-bound water arrangement and coordination are identified when the quantum nature of nuclei are considered for both bulk and interfacial water molecules. Structural properties, such as inter-/intra-molecular bond lengths, coordination numbers and H-bonding angles of bulk and interfacial water molecules here calculated, are affected by NQEs mitigating the overstructured description given by AIMD. Further evidences of an AIMD overstructured description of bulk water are in the computed IR spectra, where an increased absorption peak intensity and an increased strength of the hydrogen-bond network are alleviated by NQEs. In addition, NQEs show a valuable impact on the electronic structure of the air-water interface, reducing the total valence bandwidth and the electronic energy band-gap when passing from bulk to interfacial water. This work proves how NQEs significantly affect properties and features of the air-water interface, that are essential to accurately describe H-bonded interfacial systems.

| S-EPMC11305098 | biostudies-literature

Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics.

Project description:In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra.

| S-EPMC3419466 | biostudies-other

TAO-DFT-Based Ab Initio Molecular Dynamics.

Project description:Recently, AIMD (ab initio molecular dynamics) has been extensively employed to explore the dynamical information of electronic systems. However, it remains extremely challenging to reliably predict the properties of nanosystems with a radical nature using conventional electronic structure methods (e.g., Kohn-Sham density functional theory) due to the presence of static correlation. To address this challenge, we combine the recently formulated TAO-DFT (thermally-assisted-occupation density functional theory) with AIMD. The resulting TAO-AIMD method is employed to investigate the instantaneous/average radical nature and infrared spectra of n-acenes containing n linearly fused benzene rings (n = 2-8) at 300 K. According to the TAO-AIMD simulations, on average, the smaller n-acenes (up to n = 5) possess a nonradical nature, and the larger n-acenes (n = 6-8) possess an increasing radical nature, showing remarkable similarities to the ground-state counterparts at 0 K. Besides, the infrared spectra of n-acenes obtained with the TAO-AIMD simulations are in qualitative agreement with the existing experimental data.

| S-EPMC7674663 | biostudies-literature

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion.

Project description:We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.

| S-EPMC8197069 | biostudies-literature