Point Charge Model Research Articles

Anion-polarisation-directed short-range-order in antiperovskite Li2FeSO.

Short-range ordering in cation-disordered cathodes can have a significant effect on their electrochemical properties. Here, we characterise the cation short-range order in the antiperovskite cathode material Li2FeSO, using density functional theory, Monte Carlo simulations, and synchrotron X-ray pair-distribution-function data. We predict partial short-range cation-ordering, characterised by favourable OLi4Fe2 oxygen coordination with a preference for polar cis-OLi4Fe2 over non-polar trans-OLi4Fe2 configurations. This preference for polar cation configurations produces long-range disorder, in agreement with experimental data. The predicted short-range-order preference contrasts with that for a simple point-charge model, which instead predicts preferential trans-OLi4Fe2 oxygen coordination and corresponding long-range crystallographic order. The absence of long-range order in Li2FeSO can therefore be attributed to the relative stability of cis-OLi4Fe2 and other non-OLi4Fe2 oxygen-coordination motifs. We show that this effect is associated with the polarisation of oxide and sulfide anions in polar coordination environments, which stabilises these polar short-range cation orderings. We propose that similar anion-polarisation-directed short-range-ordering may be present in other heterocationic materials that contain cations with different formal charges. Our analysis illustrates the limitations of using simple point-charge models to predict the structure of cation-disordered materials, where other factors, such as anion polarisation, may play a critical role in directing both short- and long-range structural correlations.

The effect of immediate environment on bond strength of different bond types-A valence bond study.

The ability to design catalysis largely depends on our understanding of the electrostatic effect of the surrounding on the bonds participating in the reaction. Here, we used a simplistic model of point charges (PCs) to determine a set of rules guiding how to construct PC-bond arrangement that can strengthen or weaken different chemical bonds. Using valence bond theory to calculate the in situ bond energies, we show that the effect of the PC mainly depends on the bond's dipole moment irrespective of its type (being covalent or charge shift). That is, polar bonds are getting stronger or weaker depending on the signand location of the PC, whereas non- or weakly polar bonds become stronger or weaker depending only on the location of the PC and to a smaller extent compared with polar bonds. We also show that for polar bonds, the maximal bond strengthening and weakening effect can be achieved when the PC is placed along the bond axis, as close as possible to the more and less polarizable atom/fragment, respectively. Finally, due to the stabilizing effects of polarizability, we show that, overall, it is easier to cause bond strengthening compared with bond weakening. Particularly, for polar bonds, bond strengthening is larger than bond weakening obtained by an oppositely signed PC. These rules should be useful in the future design of catalysis in, e.g., enzyme active sites.

Spin dynamics and exchange interaction in orthoferrite TbFeO3 with non-Kramers rare-earth ion

The low-temperature spin dynamics of the orthorhombic TbFeO$_3$ perovskite has been studied. It has been found that the inelastic neutron scattering (INS) spectrum contains two modes corresponding to different sublattices in the compound. The iron subsystem orders antiferromagnetically at T$_N$ = 632 K and exhibits the high-energy magnon dispersion. Magnetic dynamics of this subsystem has been described using the linear spin wave theory and our solution yields sizable anisotropy between in-plane and out-of-plane exchange interactions. This approach was previously used to describe the magnon dispersion in the TmFeO$_3$ compound. Three non-dispersive crystal electric field levels corresponding to Tb$^{3+}$ ions have been established in the region below 40 meV at about 17, 26, and 35 meV. Study of diffuse scattering at different temperatures has elucidated the behavior of the magnetic correlation length. The behavior of the Tb$^{3+}$ ion subsystem has been numerically described in the framework of the point charge model. The numerical data agree satisfactorily with the experiment and with the general concept of the single-ion approximation applied to the rare-earth subsystem of orthorhombic perovskites.

Experimental Determination of a Single Atom Ground State Orbital through Hyperfine Anisotropy.

Historically, electron spin resonance (ESR) has provided excellent insight into the electronic, magnetic, and chemical structure of samples hosting spin centers. In particular, the hyperfine interaction between the electron and the nuclear spins yields valuable structural information about these centers. In recent years, the combination of ESR and scanning tunneling microscopy (ESR-STM) has allowed to acquire such information about individual spin centers of magnetic atoms bound atop a surface, while additionally providing spatial information about the binding site. Here, we conduct a full angle-dependent investigation of the hyperfine splitting for individual hydrogenated titanium atoms on MgO/Ag(001) by measurements in a vector magnetic field. We observe strong anisotropy in both the g factor and the hyperfine tensor. Combining the results of the hyperfine splitting with the symmetry properties of the binding site obtained from STM images and a basic point charge model allows us to predict the shape of the electronic ground state configuration of the titanium atom. Relying on experimental values only, this method paves the way for a new protocol for electronic structure analysis for spin centers on surfaces.

Analytic Linear Vibronic Coupling Method for First-Principles Spin-Dynamics Calculations in Single-Molecule Magnets.

Accurate modeling of vibronically driven magnetic relaxation from ab initio calculations is of paramount importance to the design of next-generation single-molecule magnets (SMMs). Previous theoretical studies have been relying on numerical differentiation to obtain spin-phonon couplings in the form of derivatives of spin Hamiltonian parameters. In this work, we introduce a novel approach to obtain these derivatives fully analytically by combining the linear vibronic coupling (LVC) approach with analytic complete active space self-consistent field derivatives and nonadiabatic couplings computed at the equilibrium geometry with a single electronic structure calculation. We apply our analytic approach to the computation of Orbach and Raman relaxation rates for a bis-cyclobutadienyl Dy(III) sandwich complex in the frozen-solution phase, where the solution environment is modeled by electrostatic multipole expansions, and benchmark our findings against results obtained using conventional numerical derivatives and a fully electronic description of the whole system. We demonstrate that our LVC approach exhibits high accuracy over a wide range of coupling strengths and enables significant computational savings due to its analytic, "single-shot" nature. Evidently, this offers great potential for advancing the simulation of a wide range of vibronic coupling phenomena in magnetism and spectroscopy, ultimately aiding the design of high-performance SMMs. Considering different environmental representations, we find that a point charge model shows the best agreement with the reference calculation, including the full electronic environment, but note that the main source of discrepancies observed in the magnetic relaxation rates originates from the approximate equilibrium electronic structure computed using the electrostatic environment models rather than from the couplings.

Effective magnetic fields induced by chiral phonons

In a semiclassical model, magnetic fields can originate from the orbital magnetic moments of electrons. Here, using the Biot-Savart law, we theoretically predict the effective magnetic fields induced by chiral phonons in the point-charge model. Taking tellurium as an example, it is found that by applying a temperature gradient, the average effective magnetic field per mode for a specific location within a unit cell can reach the order of 0.01 T at room temperature. We prove that the effective magnetic field induced by chiral phonons has the ability to manipulate the Curie temperature and spontaneous magnetization in a ferromagnetic material or even in a general material.

Inverse spin crossover in fluorinated Fe(1,10-phenanthroline)[formula omitted](NCS)[formula omitted] adsorbed on Cu (001) surface

Density functional theory (DFT) including van der Waals weak interaction in conjunction with the so called rotational invariant DFT+U, where U is the Hubbard interaction of the iron site, is used to show that the fluorinated spin crossover Fe(phen)2(NCS)2 molecule whether in the gas phase or adsorbed on Cu(001) surface switches from the original low spin state to the high spin state. The calculated minimal energy path by means of both the nudged elastic band method and the constrained minimization method is found to be smaller for the fluorinated molecule. Using Bader electron density analysis and a point charge model, this inversion of the spin crossover is explained in terms of electron doping of the Fe-octahedron cage which led to an increase of the Fe–N bond lengths and the distortion of the Fe(II) octahedron. Consequently, the ligand-field splitting is drastically reduced, making the high-spin ground state more stable than the low-spin state. The calculated scanning tunneling microscopy (STM) images in the Tersoff–Hamann approximation show a clear distinction between the fluorinated and the unfluorinated molecule. This theoretical prediction is awaiting future STM experimental confirmation.

Intermolecular forces at ice and water interfaces: Premelting, surface freezing, and regelation.

Using Lifshitz theory, we assess the role of van der Waals forces at interfaces of ice and water. The results are combined with measured structural forces from computer simulations to develop a quantitative model of the surface free energy of premelting films. This input is employed within the framework of wetting theory and allows us to predict qualitatively the behavior of quasi-liquid layer thickness as a function of ambient conditions. Our results emphasize the significance of vapor pressure. The ice-vapor interface is shown to exhibit only incomplete premelting, but the situation can shift to a state of complete surface melting above water saturation. The results obtained serve also to assess the role of subsurface freezing at the water-vapor interface, and we show that intermolecular forces favor subsurface ice nucleation only in conditions of water undersaturation. We show that ice regelation at ambient pressure may be explained as a process of capillary freezing, without the need to invoke the action of bulk pressure melting. Our results for van der Waals forces are exploited in order to gauge dispersion interactions in empirical point charge models of water.

The performance of OPC water model in prediction of the phase equilibria of methane hydrate.

Molecular dynamics (MD) simulations were performed to determine the three-phase coexistence line of sI methane hydrates. The MD simulations were carried out at four different pressures (4, 10, 40, and 100 MPa) by using the direct phase coexistence method. In current simulations, water was described by either TIP4P/Ice or "optimal" point charge (OPC) models and methane was described as a simple Lennard-Jones interaction site. Lorentz-Berthelot (LB) combining rules were used to calculate the parameters of the cross interactions. For the OPC model, positive deviations from the energetic LB rule were also considered based on the solubility of methane in water. For the TIP4P/Ice water model, the obtained three phase coexistence temperatures showed good agreement with experiment data at higher pressures, which is consistent with previous predictions. For the OPC water model, simulations using the classic and the modified LB parameters both showed negative deviations to the experimental values. Our results also indicated that the deviation of the T3 prediction by the OPC model was not closely correlated with the predicted melting point of ice. At 4 MPa, the modified OPC model showed a better prediction of hydrate equilibrium temperature, even better than the prediction by TIP4P/Ice. Considering the relatively higher accuracy in biomolecular MD of the OPC model, it is suggested that this model may have a better performance in hydrate MD simulations of biomolecule-based additives.

Revealing the effect of interstitial oxygen on the low-energy crystal electric field excitations of Pr3+ in 214 -nickelates

We report an inelastic neutron scattering study (INS) on the low-energy crystal electric field (CEF) excitations of ${\mathrm{Pr}}_{2\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{NiO}}_{4+\ensuremath{\delta}}$ single crystals at various temperatures. The observed low-$E$ CEF level of the O-doped sample $(x=0,\phantom{\rule{4pt}{0ex}}\ensuremath{\delta}\ensuremath{\approx}0.24)$ at $\ensuremath{\sim}5.5\phantom{\rule{4pt}{0ex}}\mathrm{meV}$ appears at significantly lower energy than that of the Sr-doped sample $(x=0.5,\phantom{\rule{4pt}{0ex}}\ensuremath{\delta}=0.0)$ at $\ensuremath{\sim}8.5\phantom{\rule{4pt}{0ex}}\mathrm{meV}$. Applying the point charge (PC) model calculation, this has been interpreted as an effect of the interstitial oxygen via lowering the local symmetry and modifying the CEF environment of the central rare earth ${\mathrm{Pr}}^{3+}$ $(^{3}H_{4})$ ions.

Niobium speciation in minerals revealed byL2,3-edges XANES spectroscopy

AbstractThe systematic mineralogy of niobium (Nb) is complex, with more than one hundred species dominated by multicomponent oxides of similar chemistry. The determination of Nb speciation in solids (i.e., the distribution between the phases and the crystal-chemical environment of Nb) is thus a challenge in geological contexts. Here, we present the first Nb L2,3-edges X-ray absorption near-edge structure (XANES) measurements on various Nb minerals and synthetic oxides with geological relevance. The interpretation of Nb L2,3-edges XANES spectra in the light of crystal-field theory shows the sensitivity of spectra to local site symmetry and electronic environment around Nb atoms. Crystal-field multiplet simulations give estimates of the 10Dq crystal-field parameter values for Nb5+, which range from 2.8 to 3.9 eV depending on Nb coordination and Nb—O distances. Rather than a 10Dq vs. R–5 relationship (where R represents the average Nb-O bond distance) expected in a point-charge model, we find a R–3 dependence with the crystal-field splitting for reference materials with octahedrally coordinated Nb. Complementary ligand-field multiplet simulations provide evidence of charge transfer between Nb and O. The contribution of the ionic and covalent characters to the Nb-O bonds is equivalent, unlike more ionic 3d metal–O bonds. This systematic characterization of the L2,3-edges XANES spectral properties of Nb provides information on the mechanisms by which Nb5+ substitutes for Fe3+, Ti4+, or Ce4+ in oxides common in geological contexts. Whereas the substitution of Nb5+ for Ce4+ does not modify the local structure of the cation site in cerianite, the substitution of Nb5+ for Ti4+ in rutile and anatase results in an increase of the cation-ligand distance and a decrease in the symmetry of the cation site. Conversely, the substitution of Nb5+ for Fe3+ in hematite and goethite results in a smaller cation site distortion. Our study demonstrates the usefulness of L2,3-edges XANES spectroscopy to determine Nb speciation in minerals to understand the processes of enrichment of this critical metal.

Can molecular simulations reliably compare homogeneous and heterogeneous ice nucleation?

In principle, the answer to the posed titular question is undoubtedly "yes." But in practice, requisite reference data for homogeneous systems have been obtained with a treatment of intermolecular interactions that is different from that typically employed for heterogeneous systems. In this article, we assess the impact of the choice of truncation scheme when comparing water in homogeneous and inhomogeneous environments. Specifically, we use explicit free energy calculations and a simple mean field analysis to demonstrate that using the "cut-and-shift" version of the Lennard-Jones potential (common to most simple point charge models of water) results in a systematic increase in the melting temperature of ice Ih. In addition, by drawing an analogy between a change in cutoff and a change in pressure, we use existing literature data for homogeneous ice nucleation at negative pressures to suggest that enhancements due to heterogeneous nucleation may have been overestimated by several orders of magnitude.

Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry.

Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue‐absorbing proteorhodopsin (BPR) and green‐absorbing proteorhodopsin (GPR). This blue/green color‐shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C14−C15 bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts.

Stress tensor and constant pressure simulation for polarizable Gaussian multipole model.

Our previous article has established the theory of molecular dynamics (MD) simulations for systems modeled with the polarizable Gaussian multipole (pGM) electrostatics [Wei et al., J. Chem. Phys. 153(11), 114116 (2020)]. Specifically, we proposed the covalent basis vector framework to define the permanent multipoles and derived closed-form energy and force expressions to facilitate an efficient implementation of pGM electrostatics. In this study, we move forward to derive the pGM internal stress tensor for constant pressure MD simulations with the pGM electrostatics. Three different formulations are presented for the flexible, rigid, and short-range screened systems, respectively. The analytical formulations were implemented in the SANDER program in the Amber package and were first validated with the finite-difference method for two different boxes of pGM water molecules. This is followed by a constant temperature and constant pressure MD simulation for a box of 512 pGM water molecules. Our results show that the simulation system stabilized at a physically reasonable state and maintained the balance with the externally applied pressure. In addition, several fundamental differences were observed between the pGM and classic point charge models in terms of the simulation behaviors, indicating more extensive parameterization is necessary to utilize the pGM electrostatics.

A New Electric Field Mill Network to Estimate Temporal Variation of Simplified Charge Model in an Isolated Thundercloud.

The gross charge distribution in an electrified cloud has already been estimated by polarity distribution of the electrostatic field on the ground surface. While either a dipole or a tripole charge structure is commonly accepted, the increase–decrease and motion of each point charge in those models are both still unclear. This paper presents a new network of electric field mills for multipoint electrostatic measurement to evaluate the temporal variations of a simple cloud charge model with second-scale resolution. Details of our newly developed equipment are described, with an emphasis on its advantages. This network was deployed in the north Kanto area of Japan and operated during the summer season in 2020. In order to simplify the relationship between cloud charge positions and the horizontal distribution of the measured electrostatic field, an isolated thundercloud is focused on. As an initial analysis, a negative point charge model is applied to an isolated cloud observed on 27 August 2020. The quantity and height of the point charge were estimated as being approximately −20 C and 7 km, respectively. The calculated charge location is generally coincident with the C-band radar echo regions. Significant correspondence is demonstrated between the intensity distribution of the electrostatic fields measured at seven sites and that calculated with estimated point charge. This result indicates the possibility to determine the amounts and positions of cloud charges inside the dipole charge structure based on multipoint measurement of the electrostatic field.

Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects.

The photophysics of green fluorescent protein (GFP) and red Kaede fluorescent protein (rKFP) are defined by the intrinsic properties of the light-absorbing chromophore and its interaction with the protein binding pocket. This work deploys photodissociation action spectroscopy to probe the absorption profiles for a series of synthetic GFP and rKFP chromophores as the bare anions and as complexes with the betaine zwitterion, which is assumed as a model for dipole microsolvation. Electronic structure calculations and energy decomposition analysis using Symmetry-Adapted Perturbation Theory are used to characterize gas-phase structures and complex cohesion forces. The calculations reveal a preponderance for coordination of betaine to the phenoxide deprotonation site predominantly through electrostatic forces. Calculations using the STEOM-DLPNO-CCSD method are able to reproduce absolute and relative vertical excitation energies for the bare anions and anion-betaine complexes. On the other hand, treatment of the betaine molecule with a point-charge model, in which the charges are computed from some common electron density population analysis schemes, show that just electrostatic and point-charge induction interactions are unable to account for the betaine-induced spectral shift. The present methodology could be applied to investigate cluster forces and optical properties in other gas-phase ion-zwitterion complexes.

Development of polarizable Gaussian multipole model

Electrostatic interactions are of fundamental importance for the structures and functions of biomolecules. Their accurate modeling is crucial in the design and development of physical models in computational studies of biomolecules. It is known that widely used point-charge models cannot capture subtle multibody effects and molecular polarization anisotropicity. Recently emerged point multipole models, in the meantime, face a so-called “polarization catastrophe” difficulty that requires artificial truncation and omission of important short-range interactions.

Crystal field effects in the zig-zag chain compound SrTm2O[formula omitted

The single ion properties of the zig-zag chain compound SrTm2O4 have been investigated using heat capacity, magnetic susceptibility, magnetization, inelastic neutron scattering, and polarized muon spectroscopy. Two crystal field models are employed to estimate the single ion properties; a Density Function Theory based model and an effective charge model based on the Hutchings point charge model. The latter describes our experimental results well. This model estimates an easy-axis anisotropy for one of the Tm3+ sites and an easy-plane anisotropy for the second site. It also predicts a mixed ground state with dominating J=0 characteristics for both sites. Additionally, muon spin rotation/relaxation (μ+SR) spectra reveal oscillations, typically a sign of long-range magnetic order. However, the temperature dependence of the precession frequency and the relaxation rates indicate that the system is in an extended critical regime and the observed relaxation is actually dynamic.

Observing Mesoscopic Nucleic Acid Capacitance Effect and Mismatch Impact via Graphene Transistors.

This work reports a molecular-scale capacitance effect of the double helical nucleic acid duplex structure for the first time. By quantitatively conducting large sample measurements of the electrostatic field effect using a type of high-accuracy graphene transistor biosensor, an unusual charge-transport behavior is observed in which the end-immobilized nucleic acid duplexes can store a part of ionization electrons like molecular capacitors, other than electric conductors. To elucidate this discovery, a cascaded capacitive network model is proposed as a novel equivalent circuit of nucleic acid duplexes, expanding the point-charge approximation model, by which the partial charge-transport observation is reasonably attributed to an electron-redistribution behavior within the capacitive network. Furthermore, it is experimentally confirmed that base-pair mismatches hinder the charge transport in double helical duplexes, and lead to directly identifiable alterations in electrostatic field effects. The bioelectronic principle of mismatch impact is also self-consistently explained by the newly proposed capacitive network model. The mesoscopic nucleic acid capacitance effect may enable a new kind of label-free nucleic acid analysis tool based on electronic transistor devices. The in situ and real-time nucleic acid detections for virus biomarkers, somatic mutations, and genome editing off-target may thus be predictable.

Unavoidable failure of point charge descriptions of electronic density changes for out-of-plane distortions

Population analyses based on point charge approximations accurately estimating the equilibrium dipole moment will systematically fail when predicting infrared intensities of out-of-plane vibrations of planar molecules, whereas models based on both charges and dipoles will always succeed. It is not a matter of how the model is devised but rather how many degrees of freedom are available for the calculation. Population analyses based on point charges are very limited in terms of the amount of meaningful chemical information they provide, whereas models employing both atomic charges and atomic dipoles should be preferred for molecular distortions. A good model should be able to correctly describe not only static, equilibrium structures but also distorted geometries in order to correctly assess information from vibrating molecules. The limitations of point charge models also hold for distortions much larger than those encountered vibrationally.