Dielectric Continuum Model Research Articles

Analytical method for calculation of the potential profiles of nitride-based resonance tunneling structures

Using the effective mass model for an electron and the dielectric continuum model, analytical solutions of the self-consistent Schr\"odinger-Poisson system of equations are obtained. Quantum mechanical theory of electronic stationary states, the oscillator strengths of quantum transitions and a method of potential profile calculation is developed for the experimentally constructed three-well resonance-tunneling structure --- a separate cascade of quantum cascade detector. For the proposed method, a comparison with the results of other methods and with the results of the experiment was carried out. A good agreement between the calculated value of the detected energy and its experimental value has been obtained, the difference being no more than $2.5\%$.

Interface optical phonons and its ternary mixed effects in ZnS/CdxZn1-xS quantum dots

Taking into account cadmium element concentrations, the interface optical (IO) phonons, electron-phonon couplings in ZnS/CdxZn1-xS quantum dots are investigated theoretically within the framework of macroscopical dielectric continuum model (MDCM) and modified random-element isodisplacement model (MREIM). The numerical results indicate that the cadmium element concentrations have important effects on the properties of IO phonons and electron-phonon interactions in a single ZnS/CdxZn1-xS quantum dot. The dependences between IO phonon frequencies and cadmium element concentrations are linearly decreases in high frequency range (HF-range), and are non-linearly decreases in low frequency range (LF-range). The numerical results also suggest that the dependent relations between the absolute value of electron-phonon coupling strengths and cadmium element concentration are linear relationship in high frequency range (HF-range), and are non-linear relationship in low frequency range (LF-range), especially in higher cadmium element concentration range.

Electron Scattering via Interface Optical Phonons with High Group Velocity in Wurtzite GaN-based Quantum Well Heterostructure

Here we present a detailed theoretical analysis of the interaction between electrons and optical phonons of interface and confined modes in a wurtzite AlN/GaN/AlN quantum well heterostructure based on the uniaxial dielectric continuum model. The formalism describing the interface and confined mode optical phonon dispersion relation, electron–phonon scattering rates, and average group velocity of emitted optical phonons are developed and numerically calculated. The dispersion relation of the interface phonons shows a convergence to the resonant phonon frequencies 577.8 and 832.3 cm−1 with a steep slope around the zone center indicating a large group velocity. At the onset of interface phonon emission, the average group velocity is small due to the large contribution of interface and confined mode phonons with close-to-zero group velocity, but eventually increases up to larger values than the bulk GaN acoustic phonon velocity along the wurtzite crystal c-axis (8 nm/ps). By adjusting the GaN thickness in the double heterostructure, the average group velocity can be engineered to become larger than the velocity of acoustic phonons at a specific electron energy. This suggests that the high group velocity interface mode optical phonons can be exploited to remove heat more effectively and reduce junction temperatures in GaN-based heterostructures.

Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model

AbstractWe demonstrate that the solvation‐layer interface condition (SLIC) continuum dielectric model for molecular electrostatics, combined with a simple solvent‐accessible‐surface‐area (SASA)‐proportional model for nonpolar solvent effects, accurately predicts solvation entropies of neutral and charged small molecules. The SLIC/SASA model has only seven fitting parameters in total and achieves this accuracy using a training set with only 20 compounds. Despite this simplicity, solvation free energies and entropies are nearly as accurate as those predicted by the more sophisticated Langevin dipoles solvation model. Surprisingly, the model automatically reproduces the negligible contribution of electrostatics to the solvation of hydrophobic compounds. Opportunities for improvement include nonpolar solvation, anion solvation entropies, and heat capacities. More molecular realism may be needed for these quantities. To enable a future, explicit‐solvent‐based assessment of the SLIC/SASA implicit‐solvent model, we predict solvation entropies for the Mobley test set, which are available as Supporting Information.

Calculating Optical Rotatory Dispersion Spectra in Solution Using a Smooth Dielectric Model.

The calculation of specific rotation of molecules in solution is probed at the coupled cluster (CC) level utilizing a continuum dielectric model based on a definition of the dielectric permittivity as a smooth function of electron density. Solvation effects are captured through polarization of Hartree-Fock (HF) molecular orbitals before subsequent calculations with the coupled cluster singles and doubles (CCSD) method. For the challenging ( S)-methyloxirane molecule, CCSD specific rotations yield an incorrect sign for the rotation in water, and the continuum model is unable to predict the wide variations in the optical rotatory dispersion (ORD) curves seen for nonpolar solvents of similar dielectric constant. In two molecules, (1 S,4 S)-norbornenone and ( S)-2-chloropropionitrile, specific rotations computed with CCSD in conjunction with implicit solvent fail to provide solvent shifts of the correct order of magnitude, indicating that the solvent response is a major contribution to the overall solvation effect.

Real-time detection of alcohol vapors and volatile organic compounds via optical electronic nose using carbon dots prepared from rice husk and density functional theory calculation

Rice husk, an agricultural waste that currently finds few uses, is rich in cellulose-based materials and silica. In this work, a simple one-pot method for preparing carbon dots and mesoporous silica from rice husk was developed, using hydrothermal and calcination methods. The carbon dots exhibited blue emission with excellent photostability, and had a diameter of 4–5 nm and a quantum yield of 3%. They were demonstrated to be capable of detecting alcohol vapors at room temperature, and of distinguishing between methanol, ethanol, and several volatile organic compounds when used as the sensing layer in an optical electronic nose system. The alcohol content of a commercial beverage was successfully determined using the carbon dot-integrated electronic nose. The solvation effect of the alcohol vapors on the electronic absorption spectra of model carbon dot structures was illustrated using time-dependent density functional theory with the dielectric polarizable continuum model. The UV–vis and computational results confirmed that the sensing mechanism of carbon dots is through the modulation of their optical absorbance governed by polar-polar interfacial interactions. This was experimental and computational demonstration of carbon dot sensing of vapors. Their excellent biocompatibility suggests biomedical applications, in addition to sensing. The production of two functional materials from a single low-value waste source was demonstrated.

A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

<p style='text-indent:20px;'>The nonlocal modified Poisson-Boltzmann equation (NMPBE) is one important variant of a commonly-used dielectric continuum model, Poisson-Boltzmann equation (PBE). In this paper, we use a nonlinear block relaxation method to develop a new nonlinear solver for the nonlinear equation of <inline-formula><tex-math id="M1">\begin{document} $\Phi $ \end{document}</tex-math></inline-formula> and thus a new NMPBE solver, which is then programmed as a software package in <inline-formula><tex-math id="M2">\begin{document} $\texttt{C}\backslash\texttt{C++}$ \end{document}</tex-math></inline-formula>, <inline-formula><tex-math id="M3">\begin{document} $\texttt{Fortran}$ \end{document}</tex-math></inline-formula> and <inline-formula><tex-math id="M4">\begin{document} $\texttt{Python}$ \end{document}</tex-math></inline-formula> for computing the electrostatics of a protein in a symmetric 1:1 ionic solvent. Numerical tests validate the new package and show that the new solver can improve the efficiency by at least <inline-formula><tex-math id="M5">\begin{document}$ 40\%$ \end{document}</tex-math></inline-formula> than the finite element NMPBE solver without compromising solution accuracy.

An accelerated nonlocal Poisson‐Boltzmann equation solver for electrostatics of biomolecule

The nonlocal modified Poisson-Boltzmann equation (NMPBE) is one important variant of a commonly used dielectric continuum model, the Poisson-Boltzmann equation (PBE), for computing electrostatics of biomolecules. In this paper, an accelerated NMPBE solver is constructed by finite element and finite difference hybrid techniques. It is then programmed as a software package for computing electrostatic solvation and binding free energies for a protein in a symmetric 1:1 ionic solvent. Numerical results validate the new solver and its numerical stability. They also demonstrate that the new solver has much better performance than the corresponding finite element solver in terms of computer CPU time. Furthermore, they show that the binding free energies produced by NMPBE can match chemical experiment data better than those by PBE.

Coupled Cluster Theory Combined with Reference Interaction Site Model Self-Consistent Field Explicitly Including Spatial Electron Density Distribution.

Calculating the geometry and energy of a molecule in a solution is one of the most important tasks in chemistry. However, performing an accurate calculation in a solution is still a difficult task because the electronic structure and solute-solvent interactions are required to be accurately evaluated with an efficient computational cost. To overcome this difficulty, we proposed the coupled cluster with single and double excitations and perturbative triple excitations combined with the reference interaction site model (RISM) by employing our fitting approach. Our method correctly reproduced the relative stabilities of 1,2,3-triazole, isonicotinic acid, cytosine, and 6-chloro-2-pyridone in the aqueous phase, whereas the dielectric continuum model provided incorrect results for isonicotinic acid and 6-chloro-2-pyridone. Our method provided accurate results because the RISM captured the local solvation structure, such as hydrogen bonds.

Interface optical phonons and their electron-phonon interactions in ZnS/CdS multi-shell spherical quantum dots

The properties of interface optical phonons and their electron-phonon interactions in ZnS/CdS multi-shell spherical quantum dots are studied by adopting dielectric continuum model. The dispersion curves and electron-phonon coupling strengths for interface optical phonons in ZnS/CdS multi-shell dots are calculated and analyzed in detail. It is shown that the number of interface optical phonon branches increase with the increase of layers of multi-shell quantum dots. The number of interface optical phonons increase two branches for increasing one layer material. The dispersions of interface optical phonon with low quantum number l are weak. The electron-interface optical phonon interactions are mainly localized at hetero-interfaces. The interface optical phonons with low quantum number l have important contribution to electron-interface optical phonon interactions.

Raman analysis of phonon modes in a short period AlN/GaN superlattice

AlN/GaN-based optoelectronic devices have been the subject of intense research underlying the commercialization of efficient devices. Areas of considerable interest are the study of their lattice dynamics, phonon transport, and electron-phonon interactions specific to the interface of these heterostructures which results in additional optical phonon modes known as interface phonon modes. In this study, the framework of the dielectric continuum model (DCM) has been used to compare and analyze the optical phonon modes obtained from experimental Raman scattering measurements on AlN/GaN short-period superlattices. We have observed the localized E2(high), A1(LO) and the E1(TO) modes in superlattice measurements at frequencies shifted from their bulk values. To the best of our knowledge, the nanostructures used in these studies are among the smallest yielding useful Raman signatures for the interface modes. In addition, we have also identified an additional spread of interface phonon modes in the TO range resulting from the superlattice periodicity. The Raman signature contribution from the underlying AlxGa1-xN ternary has also been observed and analyzed. A temperature calibration was done based on Stokes/anti-Stokes ratio of A1(LO) using Raman spectroscopy in a broad operating temperature range. Good agreement between the experimental results and theoretically calculated calibration plot predicted using Bose-Einstein statistics was obtained.

Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions.

Understanding the nature of ionic hydration at a fundamental level has eluded scientists despite intense interest for nearly a century. In particular, the microscopic origins of the asymmetry of ion solvation thermodynamics with respect to the sign of the ionic charge remains a mystery. Here, we determine the response of accurate quantum mechanical water models to strong nanoscale solvation forces arising from excluded volumes and ionic electrostatic fields. This is compared to the predictions of two important limiting classes of classical models of water with fixed point changes, differing in their treatment of "lone pair" electrons. Using the quantum water model as our standard of accuracy, we find that a single fixed classical treatment of lone pair electrons cannot accurately describe solvation of both apolar and cationic solutes, emphasizing the need for a more flexible description of local electronic effects in solvation processes. However, we explicitly show that all water models studied respond to weak long-ranged electrostatic perturbations in a manner that follows macroscopic dielectric continuum models, as would be expected. We emphasize the importance of these findings in the context of realistic ion models, using density functional theory and empirical models, and discuss the implications of our results for quantitatively accurate reduced descriptions of solvation in dielectric media.

Computation of forces arising from the polarizable continuum model within the domain-decomposition paradigm.

The domain-decomposition (dd) paradigm, originally introduced for the conductor-like screening model, has been recently extended to the dielectric Polarizable Continuum Model (PCM), resulting in the ddPCM method. We present here a complete derivation of the analytical derivatives of the ddPCM energy with respect to the positions of the solute's atoms and discuss their efficient implementation. As it is the case for the energy, we observe a quadratic scaling, which is discussed and demonstrated with numerical tests.

Wobbled electronic properties of lithium clusters: Deterministic approach through first principles

The innate tendency to form dendritic growth promoted through cluster formation leading to the failure of a Li-ion battery system have drawn significant attention of the researchers towards the effective destabilization of the cluster growth through selective implementation of electrolytic media such as acetonitrile (MeCN). In the present work, using first principles density functional theory and continuum dielectric model, we have investigated the origin of oscillatory nature of binding energy per atom of Lin (n ≤ 8) under the influence of MeCN. In the gas phase, we found that static mean polarizability is strongly correlated with binding energy and shows oscillatory nature with cluster size due to the open shell of Lin cluster. However, in acetonitrile medium, the binding energy has been correlated with electrostatic Lin−MeCN interaction and it has been found that both of them possess wobbled behavior characterized by the cluster size.

A theoretical investigation on bio-transformation of third generation anti-cancer drug Heptaplatin and its interaction with DNA purine bases

Heptaplatin is an approved platinum based cytostatic drug for the treatment of gastric cancers. The hydrolytic bio-transformation of Heptaplatin and the platination processes of guanine (G) and adenine (A) with resulting mono and di-aquated species of Heptaplatin have been investigated using density functional theory (DFT) combined with the conductor like dielectric continuum model (CPCM) approach, to spotlight the drug activation energy profiles and their binding mechanisms. The stationary points on the potential energy surfaces were fully optimized and characterized. The mono-functional binding of Heptaplatin, guanine as target over adenine due to electronic factors and more favorable hydrogen-bonds pattern.

The COSMO and COSMO‐RS solvation models

The conductor‐like screening model COSMO, a variant of the dielectric continuum solvation models, has become very popular due to its algorithmic simplicity, numerical stability, and its great insensitivity with respect to outlying charge errors. The advanced model COSMO‐RS, i.e., COSMO for realistic solvation, is a statistical thermodynamics theory based on COSMO polarization charge densities, which overcomes many of the limitations and theoretical shortcomings of dielectric continuum models. Due to its ability to treat mixtures at variable temperatures, it has become very popular in chemical engineering and in wide areas of physical and medicinal chemistry. COSMO‐RS may currently be considered the most accurate model for the prediction of solvation energies. This article provides a short description of the basic concepts of both models, of the differences with other solvation models, and of their application areas. Finally, Direct‐COSMO‐RS, a recent direct integration of the COSMO‐RS concept into quantum chemical calculations, is briefly described. WIREs Comput Mol Sci 2018, 8:e1338. doi: 10.1002/wcms.1338This article is categorized under: Structure and Mechanism &gt; Computational Materials Science

Optimal Tuning of Range-Separated Hybrids for Solvated Molecules with Time-Dependent Density Functional Theory.

The applicability range of density functional theory (DFT) can be improved with no additional parametrization by imposing some exact conditions. Enforcing equality between the orbital energy of the highest occupied Kohn-Sham orbital and ionization energy, determined from the total energy difference between neutral and ionized states (ΔKS), leads to the concept of optimally tuned range-separated hybrid functionals. Here, we present an alternative tuning scheme for range-separated hybrid functionals based on enforcing the equality between the ΔKS ionization energy and the ionization energy calculated by means of the time-dependent DFT using the concept of ionization as an excitation to the distant center (OT-IEDC scheme). The scheme can be naturally applied to solvated systems described either within the explicit solvation or dielectric continuum models. We test the performance of the scheme on a benchmark set of molecules. We further show that the scheme allows for reliably modeling liquid phase photoemission spectra.

Self-Consistent Calculation of Potential Profile of GaN/AlN Resonace Tunnelling Structures

For resonant tunneling structure with GaN – potential wells and AlN – potential barriers, calculation of internal fields caused by piezoelectric and spontaneous polarization was carried. In the model the effective mass of an electron and a dielectric continuum model using finite difference method self-consistent solutions of the Schrödinger and Poisson system of equations taking into account the contribution of piezoelectric and spontaneous polarizations was found.Based on the found solutions of the Schrödinger and Poisson system of equations for resonance tunneling structure, which functioned as a cascade experimentally realized a quantum cascade detector, calculation of the potential profile and the electron energy spectrum was carried. It was found, that calculated value of detected energy is different from the experimentally obtained not more than 3 %.

Orthogonal Electric Field Measurements near the Green Fluorescent Protein Fluorophore through Stark Effect Spectroscopy and pKa Shifts Provide a Unique Benchmark for Electrostatics Models.

Measurement of the magnitude, direction, and functional importance of electric fields in biomolecules has been a long-standing experimental challenge. pKa shifts of titratable residues have been the most widely implemented measurements of the local electrostatic environment around the labile proton, and experimental data sets of pKa shifts in a variety of systems have been used to test and refine computational prediction capabilities of protein electrostatic fields. A more direct and increasingly popular technique to measure electric fields in proteins is Stark effect spectroscopy, where the change in absorption energy of a chromophore relative to a reference state is related to the change in electric field felt by the chromophore. While there are merits to both of these methods and they are both reporters of local electrostatic environment, they are fundamentally different measurements, and to our knowledge there has been no direct comparison of these two approaches in a single protein. We have recently demonstrated that green fluorescent protein (GFP) is an ideal model system for measuring changes in electric fields in a protein interior caused by amino acid mutations using both electronic and vibrational Stark effect chromophores. Here we report the changes in pKa of the GFP fluorophore in response to the same mutations and show that they are in excellent agreement with Stark effect measurements. This agreement in the results of orthogonal experiments reinforces our confidence in the experimental results of both Stark effect and pKa measurements and provides an excellent target data set to benchmark diverse protein electrostatics calculations. We used this experimental data set to test the pKa prediction ability of the adaptive Poisson-Boltzmann solver (APBS) and found that a simple continuum dielectric model of the GFP interior is insufficient to accurately capture the measured pKa and Stark effect shifts. We discuss some of the limitations of this continuum-based model in this system and offer this experimentally self-consistent data set as a target benchmark for electrostatics models, which could allow for a more rigorous test of pKa prediction techniques due to the unique environment of the water-filled GFP barrel compared to traditional globular proteins.

Engineering Redox Potential of Lithium Clusters for Electrode Material in Lithium-Ion Batteries

Low negative electrode potential and high reactivity makes lithium (Li) ideal candidate for obtaining highest possible energy density among other materials. In this work we show a novel route with which the overall electrode potential could significantly be enhanced through selection of cluster size. Using first principles density functional theory and continuum dielectric model, we studied free energy and redox potential as well as investigated relative stability of Lin (n ≤ 8) clusters in both gas phase and solution. We found that Li3 has the lowest negative redox potential (thereby highest overall electrode potential) suggesting that cluster based approach could provide a novel way of engineering the next generation battery technology. The microscopic origin of Li3 cluster’s superior performance is related to two major factors: gas phase ionization and difference between solvation free energy for neutral and positive ion. Taken together, the present study provides insight into the engineering of redox potential in battery and could stimulate further work in this direction.