Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond.

ABSTRACT: Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable in accuracy to those with much more complex functional forms, despite having drastically fewer parameters. The parametrization protocol has been implemented as part of the Q-Force automated workflow and requires only a quantum mechanical Hessian calculation as reference data, hence allowing it to be easily extended to a variety of molecular systems beyond water, which we demonstrate on a selection of small molecules with different symmetries.

SUBMITTER: Sami S

PROVIDER: S-EPMC11229074 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond.

Sami Selim S LaCour R Allen RA Heindel Joseph P JP Head-Gordon Teresa T

The journal of physical chemistry letters 20240620 26

Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable ...[more]

PMID: 38900596

Similar Datasets

Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis.

Project description:The energetics of water molecules in proteins is studied using the water placement software Dowser. We compared the water position predictions for 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules. From the analysis of the outputs of Dowser with variable parameters and comparison with experimental X-ray data, we derived an estimate of the average dipole moment of water molecules located in the internal cavities of the protein and their binding energies. The water parameters thus obtained from the experimental data are then analyzed within the framework of charge-scaling theory developed recently by this group; the parameters are shown to be in good agreement with the predictions that the theory makes for the dipole moment in a protein environment. The water dipole in the protein environment is found to be much different from that in the bulk and in such models as SPC or TIPnP. The role of charge scaling due to electronic polarizability of the protein is discussed.

| S-EPMC4196742 | biostudies-other

Toward Accurate Ab Initio Ground-State Potential Energy and Electric Dipole Moment Functions of Carbon Monoxide.

Project description:Accurate potential energy and electric dipole moment functions of the CO molecule in its ground electronic state X1Σ+ have been obtained using the single-reference coupled-cluster approach, up to the CCSDTQP level of approximation, in conjunction with the augmented core-valence correlation-consistent basis sets, aug-cc-pCVnZ, up to octuple-zeta quality. The scalar relativistic, adiabatic, and nonadiabatic effects were discussed. The ab initio predicted functions were compared with their experimentally derived counterparts.

| S-EPMC11500290 | biostudies-literature

Observation of the Low-Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces.

Project description:Using the helium nanodroplet isolation setup at the ultrabright free-electron laser source FELIX in Nijmegen (BoHeNDI@FELIX), the intermolecular modes of water dimer in the frequency region from 70 to 550 cm-1 were recorded. Observed bands were assigned to donor torsion, acceptor wag, acceptor twist, intermolecular stretch, donor torsion overtone, and in-plane and out-of-plane librational modes. This experimental data set provides a sensitive test for state-of-the-art water potentials and dipole moment surfaces. Theoretical calculations of the IR spectrum are presented using high-level quantum and approximate quasiclassical molecular dynamics approaches. These calculations use the full-dimensional ab initio WHHB potential and dipole moment surfaces. Based on the experimental data, a considerable increase of the acceptor switch and a bifurcation tunneling splitting in the librational mode is deduced, which is a consequence of the effective decrease in the tunneling barrier.

| S-EPMC7687217 | biostudies-literature

Simple stochastic model for geomagnetic excursions and reversals reproduces the temporal asymmetry of the axial dipole moment.

Project description:We present a simple model for the axial dipole moment (ADM) of the geomagnetic field based on a stochastic differential equation for two coupled particles in a biquadratic potential, subjected to Gaussian random perturbations. This model generates aperiodic reversals and excursions separated by stable polarity periods. The model reproduces the temporal asymmetry of geomagnetic reversals, with slower decaying rates before the reversal and faster growing rates after it. This temporal asymmetry is possible because our model is out of equilibrium. The existence of a thermal imbalance between the two particles sets a preferential sense for the energy flux and renders the process irreversible.

| S-EPMC7958179 | biostudies-literature

Dipole-Moment Modulation in New Incommensurate Ferrocene.

Project description:Despite 70 years of research on metallocenes and their applications, there are still unresolved regions in its phase diagram of the prototypic sandwich compound, ferrocene Fe2+[C5H5]-2 (FeCp2), and its molecular 5-fold symmetry cannot be reconciled with the dielectric response of this crystal. We found a new phase I″ of ferrocene, which reveals the relationships between the molecular conformation, intermolecular interactions, and electric permittivity of this compound. Between 172.8 and 163.5 K, the conformational disorder of ferrocene molecules transforms into the incommensurate modulation. The structure of phase I″ is described in the (3+2)-dimensional superspace, where the molecular conformations, rotations and inclinations of the Cp rings, molecular tilts, and displacements of the Fe2+ cations, as well as the CH···π bonds in the crystal environment, are modulated. These geometric changes combine into the FeCp2 bending distortion, breaking the 5-fold symmetry and generating waves of molecular dipole moments with their amplitudes approaching 4 × 10-30 C·m.

| S-EPMC10084461 | biostudies-literature

Simple and Accurate Exchange Energy for Density Functional Theory.

Project description:A non-empirical exchange functional based on an interpolation between two limits of electron density, slowly varying limit and asymptotic limit, is proposed. In the slowly varying limit, we follow the study by Kleinman from 1984 which considered the response of a free-electron gas to an external periodic potential, but further assume that the perturbing potential also induces Bragg diffraction of the Fermi electrons. The interpolation function is motivated by the exact exchange functional of a hydrogen atom. Combined with our recently proposed correlation functional, tests on 56 small molecules show that, for the first-row molecules, the exchange-correlation combo predicts the total energies four times more accurately than the presently available Quantum Monte Carlo results. For the second-row molecules, errors of the core electrons exchange energies can be corrected, leading to the most accurate first- and second-row molecular total energy predictions reported to date despite minimal computational efforts. The calculated bond energies, zero point energies, and dipole moments are also presented, which do not outperform other methods.

| S-EPMC7436057 | biostudies-literature

One-Step Fabrication of Hot-Water-Repellent Surfaces.

Project description:Hot-water repellency is of great challenge on traditional superhydrophobic surfaces due to the condensation of tiny droplets within the cavities of surface textures, which builds liquid bridges to connect the substrate and hot water and thus destroys the surface water-repellence performance. For the unique structural features and scales, current approaches to fabricate surfaces with hot-water repellency are always complicated and modified by fluorocarbon. Here, we propose a facile and fluorine-free one-step vapor-deposition method for fabricating excellent hot-water-repellent surfaces, which at room temperature even repel water droplets of temperature up to 90 °C as well as other normal-temperature droplets with surface tension higher than 48.4 mN/m. We show that whether the unique hot-water repellency is achieved depends on a trade-off between the solid-liquid contact time and hot-vapor condensation time, which determines the probability of formation of liquid bridges between the substrate and hot-water. Moreover, the designed surfaces exhibit excellent self-cleaning performance in some specific situations, such as oil medium, hot water and condensation environments. We envision that this facile and fluorine-free strategy for fabricating excellent hot-water-repellent surfaces could be valuable in popularizing their practical applications.

| S-EPMC9221071 | biostudies-literature

Dipole moment background measurement and suppression for levitated charge sensors.

Project description:Optically levitated macroscopic objects are a powerful tool in the field of force sensing, owing to high sensitivity, absolute force calibration, environmental isolation, and the advanced degree of control over their dynamics that have been achieved. However, limitations arise from the spurious forces caused by electrical polarization effects that, even for nominally neutral objects, affect the force sensing because of the interaction of dipole moments with gradients of external electric fields. Here, we introduce a technique to measure, model, and eliminate dipole moment interactions, limiting the performance of sensors using levitated objects. This process leads to a noise-limited measurement with a sensitivity of 3.3 × 10-5 e. As a demonstration, this is applied to the search for unknown charges of a magnitude much below that of an electron or for exceedingly small unbalances between electron and proton charges.

| S-EPMC9565793 | biostudies-literature

Large dipole moment induced efficient bismuth chromate photocatalysts for wide-spectrum driven water oxidation and complete mineralization of pollutants.

Project description:Herein, a wide-spectrum (∼678 nm) responsive Bi8(CrO4)O11 photocatalyst with a theoretical solar spectrum efficiency of 42.0% was successfully constructed. Bi8(CrO4)O11 showed highly efficient and stable photocatalytic water oxidation activity with a notable apparent quantum efficiency of 2.87% (420 nm), superior to many reported wide-spectrum driven photocatalysts. Most remarkably, its strong oxidation ability also enables the simultaneous degradation and complete mineralization for phenol, and its excellent performance is about 23.0 and 2.9 times higher than CdS and P25-TiO2, respectively. Its high activity is ascribed to the giant internal electric field induced by its large crystal dipole, which accelerates the rapid separation of photogenerated electron-hole pairs. Briefly, the discovery of wide-spectrum bismuth chromate and the mechanism of exponentially enhanced photocatalytic performance by increasing the crystal dipole throw light on improving solar energy conversion.

| S-EPMC8289005 | biostudies-literature

Ion and Site Correlations of Charge Regulating Surfaces: A Simple and Accurate Theory.

Project description:Charge regulation is fundamental in most chemical, geochemical, and biochemical systems. Various mineral surfaces and proteins are well-known to change their charge state as a function of the activity of the hydronium ions, that is, the pH. Besides being modulated by the pH, the charge state is sensitive to salt concentration and composition due to screening and ion correlations. Given the importance of electrostatic interactions, a reliable and straightforward theory of charge regulation would be of utmost importance. This Article presents a theory that accounts for salt screening, site, and ion correlations. Our approach shows an impeccable agreement as compared to Monte Carlo simulations and experiments of 1:1 and 2:1 salts. We furthermore disentangle the relative importance of site-site, ion-ion, and ion-site correlations. Contrary to previous claims, we find that ion-site correlations for the studied cases are subdominant to the two other correlation terms.

| S-EPMC10249413 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data