Drude Oscillator Research Articles

Optical properties and electronic structure of epitaxial uranium films

Uranium exhibits high chemical activity. The preparation of single crystalline uranium films via molecular beam epitaxy, followed by in situ characterization under ultrahigh vacuum condition, effectively avoids sample contamination caused by the environmental atmosphere. In this work, single crystalline uranium films were grown on the W(110) surface by a deflected electron beam evaporator. The optical constants of the W(110) substrate and the uranium films were obtained through in situ ultrahigh vacuum spectroscopic ellipsometry, while the electronic structure of uranium films was measured by angle-resolved photoemission spectroscopy (ARPES). Notably, the optical constants of uranium film differ from those previously reported measured by the ex situ experiments. The band structure and optical constants of the uranium film were calculated by the ab initio method, and theoretical calculations were compared with the experimental results. The calculated band structure of α-U is consistent with the bulk electronic structure of uranium films measured by ARPES, except for a surface-state-like feature. The parameters of the Drude oscillator derived from the ellipsometric fitting were used to revise the calculated optical constants, which obviously improves the accuracy of the calculations. Our study provides the most strictly fundamental data of the uranium up to now.

A Simple Model for the Pauli Repulsion with Possible Utility in QM, MM and Chemical Education.

The Pauli repulsion is the intermolecular force responsible for the volume and low compressibility of condensed-phase matter at normal conditions. A simple model for this force is presented, wherein per-atom electron densities are represented as spherical charge distributions that are prevented from significantly overlapping. In the example of two noble gas atoms approaching one another beyond their van der Waals radii, the distance between the centers of the electronic charge distributions becomes larger than the distance between the nuclei, giving rise to an unfavorable electrostatic interaction. For the purpose of calculating this interaction, the model is further simplified by representing the per-atom electron density as a negative point charge, loosely inspired by the classical Drude oscillator. The dispersion interaction is simplified to an R-6 term, centered on the aforementioned point charges. Despite the gross simplicity of the resulting formalism, near-quantitative agreement with high-level QM interaction energies of noble gas dimers is achieved. Accordingly, the present model is thought to have utility in force fields, in post-HF and post-DFT dispersion corrections, and in chemical education.

Application of the CL&P-Pol polarizable force field in the determination of the excess chemical potential of thiophene within the [C4mim] [BF4, Cl, Br, CH3COO] ionic liquids

The combustion of fossil fuels is an important source of air pollution due to the presence of sulfur-based compounds. In this regard, a reliable atomistic forcefield is required in order to provide insights on solute-solvent interactions, and in designing high aromatic sulfur extracting solvents. In the present work, the excess chemical potentials of thiophene within four 1-butyl-3-methylimidazolium-based ionic liquids were evaluated through the free energy perturbation with replica exchange molecular dynamics methodology by using the CL&Pol polarizable force fields based on Drude oscillators. First, in order to validate the accuracy of the polarizable force fields, a series of thermodynamic properties of pure ionic liquids such as diffusion coefficient, liquid density, dielectric constant, and heat of vaporization were computed using the CL&Pol force field and compared against experimental values. The results from the calculated thiophene excess chemical potential values, indicated that the [C4mim][CH3COO] ionic liquid presents the more favorable excess chemical potential (higher solubility) with respect to the thiophene molecule at both 300 K and 343 K in comparison to the other ionic liquids studied. The structural analysis revealed that the ionic liquid anion interacts more closely and with well-defined RDF peaks with the thiophene molecule, the larger anions present higher surrounding particle densities with the thiophene molecules (solvation shell), while the monoatomic anions interact preferentially with the hydrogens close to the sulfur thiophene atom; In contrast no marked solvation layers were observed with the ionic liquid cations.

Quantum Drude oscillators coupled with Coulomb potential as an efficient model for bonded and non-covalent interactions in atomic dimers.

The quantum Drude oscillator (QDO) model has been widely used as an efficient surrogate to describe the electric response properties of matter as well as long-range interactions in molecules and materials. Most commonly, QDOs are coupled within the dipole approximation so that the Hamiltonian can be exactly diagonalized, which forms the basis for the many-body dispersion method [Phys. Rev. Lett. 108, 236402 (2012)]. The dipole coupling is efficient and allows us to study non-covalent many-body effects in systems with thousands of atoms. However, there are two limitations: (i) the need to regularize the interaction at short distances with empirical damping functions and (ii) the lack of multipolar effects in the coupling potential. In this work, we convincingly address both limitations of the dipole-coupled QDO model by presenting a numerically exact solution of the Coulomb-coupled QDO model by means of quantum Monte Carlo methods. We calculate the potential-energy surfaces of homogeneous QDO dimers, analyzing their properties as a function of the three tunable parameters: frequency, reduced mass, and charge. We study the coupled-QDO model behavior at short distances and show how to parameterize this model to enable an effective description of chemical bonds, such as the covalent bond in the H2 molecule.

GAFF-Based Polarizable Force Field Development and Validation for Ionic Liquids.

Ionic liquids (ILs) have been used in many applications, including gas separations, electrochemistry, lubrication, and catalysis. Understanding how the different properties of ILs are related to their chemical structure and composition is crucial for these applications. Experimental investigations often provide limited insights and can be tedious in exploring a range of state points. Therefore, molecular simulations have emerged as a powerful tool that not only offers a microscopic perspective but also enables rapid screening and prediction of physical properties. The accuracy of these predictions, however, depends on the quality of the intermolecular potentials (force fields) used. The widely used classical fixed charge models, such as GAFF, OPLS, and CL&P, are popular due to their simplicity and computational efficiency. However, it has been shown that the use of integer charges with these classical models leads to sluggish dynamics. The use of scaled charge models can improve the dynamics, but these mean-field approaches are unable to account for polarization effects explicitly. Several different approaches have been proposed to include polarizability in IL force fields. In this work, we follow the protocol of the CL&Pol model to develop a Drude oscillator model based on the GAFF force field (Goloviznina, K., et al. J. Chem. Theory Comput. 2019, 15, 5858). We compare the performance of the model for eight imidazolium- and pyrrolidinium-based ILs against that of other models. We find that the new model provides reasonable estimations of density, self-diffusivity, and structural properties for these ILs and suggests a relatively simple way of extending the general GAFF model to more ILs.

Second quantization of many-body dispersion interactions for chemical and biological systems

The many-body dispersion (MBD) framework is a successful approach for modeling the long-range electronic correlation energy and optical response of systems with thousands of atoms. Inspired by field theory, here we develop a second-quantized MBD formalism (SQ-MBD) that recasts a system of atomic quantum Drude oscillators in a Fock-space representation. SQ-MBD provides: (i) tools for projecting observables (interaction energy, transition multipoles, polarizability tensors) on coarse-grained representations of the atomistic system ranging from single atoms to large structural motifs, (ii) a quantum-information framework to analyze correlations and (non)separability among fragments in a given molecular complex, and (iii) a path toward the applicability of the MBD framework to molecular complexes with even larger number of atoms. The SQ-MBD approach offers conceptual insights into quantum fluctuations in molecular systems and enables direct coupling of collective plasmon-like MBD degrees of freedom with arbitrary environments, providing a tractable computational framework to treat dispersion interactions and polarization response in intricate systems.

Modulating the optical behaviour of metallic vanadium dioxide by adjusting the number of Drude oscillators

Modulating the optical behaviour of metallic vanadium dioxide by adjusting the number of Drude oscillators

Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators

Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators

Universal Pairwise Interatomic van der Waals Potentials Based on Quantum Drude Oscillators.

Repulsive short-range and attractive long-range van der Waals (vdW) forces play an appreciable role in the behavior of extended molecular systems. When using empirical force fields, the most popular computational methods applied to such systems, vdW forces are typically described by Lennard-Jones-like potentials, which unfortunately have a limited predictive power. Here, we present a universal parameterization of a quantum-mechanical vdW potential, which requires only two free-atom properties─the static dipole polarizability α1 and the dipole-dipole C6 dispersion coefficient. This is achieved by deriving the functional form of the potential from the quantum Drude oscillator (QDO) model, employing scaling laws for the equilibrium distance and the binding energy, and applying the microscopic law of corresponding states. The vdW-QDO potential is shown to be accurate for vdW binding energy curves, as demonstrated by comparing to the ab initio binding curves of 21 noble-gas dimers. The functional form of the vdW-QDO potential has the correct asymptotic behavior at both zero and infinite distances. In addition, it is shown that the damped vdW-QDO potential can accurately describe vdW interactions in dimers consisting of group II elements. Finally, we demonstrate the applicability of the atom-in-molecule vdW-QDO model for predicting accurate dispersion energies for molecular systems. The present work makes an important step toward constructing universal vdW potentials, which could benefit (bio)molecular computational studies.

Molecular Modeling of Water-in-Salt Electrolytes: A Comprehensive Analysis of Polarization Effects and Force Field Parameters in Molecular Dynamics Simulations.

Accurate modeling of highly concentrated aqueous solutions, such as water-in-salt (WiS) electrolytes in battery applications, requires proper consideration of polarization contributions to atomic interactions. Within the force field molecular dynamics (MD) simulations, the atomic polarization can be accounted for at various levels. Nonpolarizable force fields implicitly account for polarization effects by incorporating them into their van der Waals interaction parameters. They can additionally mimic electron polarization within a mean-field approximation through ionic charge scaling. Alternatively, explicit polarization description methods, such as the Drude oscillator model, can be selectively applied to either a subset of polarizable atoms or all polarizable atoms to enhance simulation accuracy. The trade-off between simulation accuracy and computational efficiency highlights the importance of determining an optimal level of accounting for atomic polarization. In this study, we analyze different approaches to include polarization effects in MD simulations of WiS electrolytes, with an example of a Na-OTF solution. These approaches range from a nonpolarizable to a fully polarizable force field. After careful examination of computational costs, simulation stability, and feasibility of controlling the electrolyte properties, we identify an efficient combination of force fields: the Drude polarizable force field for salt ions and non-polarizable models for water. This cost-effective combination is sufficiently flexible to reproduce a broad range of electrolyte properties, while ensuring simulation stability over a relatively wide range of force field parameters. Furthermore, we conduct a thorough evaluation of the influence of various force field parameters on both the simulation results and technical requirements, with the aim of establishing a general framework for force field optimization and facilitating parametrization of similar systems.

Optimized Quantum Drude Oscillators for Atomic and Molecular Response Properties.

The quantum Drude oscillator (QDO) is an efficient yet accurate coarse-grained approach that has been widely used to model electronic and optical response properties of atoms and molecules as well as polarization and dispersion interactions between them. Three effective parameters (frequency, mass, and charge) fully characterize the QDO Hamiltonian and are adjusted to reproduce response properties. However, the soaring success of coupled QDOs for many-atom systems remains fundamentally unexplained, and the optimal mapping between atoms/molecules and oscillators has not been established. Here we present an optimized parametrization (OQDO) where the parameters are fixed by using only dipolar properties. For the periodic table of elements as well as small molecules, our model accurately reproduces atomic (spatial) polarization potentials and multipolar dispersion coefficients, elucidating the high promise of the presented model in the development of next-generation quantum-mechanical force fields for (bio)molecular simulations.

SERS sensing of Metanil yellow in turmeric solution using self-organized nanoparticle arrays grown on Ion beam patterned soda-lime glass

Metanil yellow is a potential carcinogen that is commonly used as a food adulterant in turmeric powder. In this study, we detected Metanil Yellow from turmeric powder solution using a Surface Enhanced Raman Spectroscopy (SERS) substrate based on nano patterned soda-lime glass. Low amplitude ripples with an average wavelength around 65 nm was produced on commercially available soda-lime glass using low energy argon ion beam irradiation. Large area SERS templates were produced by growing self-organized ordered Ag nanoparticles on the rippled soda-lime glass. The optical analysis of the produced substrates shows the anisotropic plasmonic response and better Localized Surface Plasmon Resonance (LSPR) activity than Ag nanoparticles grown on rippled Si substrate. A biaxial layer consisting of Lorentz and Drude oscillators describes the real and imaginary parts of the dielectric function. The SERS analysis using Crystal Violet (CV) molecules demonstrates a five-fold improvement in the efficiency of silver grown on glass ripples than silver grown on Si ripples. We have tested the substrate for detecting Metanil yellow up to 10-6 M concentration in the water. Further, using the substrate, up to 10-4 M concentration of Metanil Yellow is detected from the turmeric solution.

Symmetrized Drude Oscillator Force Fields Improve Numerical Performance of Polarizable Molecular Dynamics

Drude oscillator potentials are a popular and computationally efficient class of polarizable models that represent each polarizable atom as a positively charged Drude core harmonically bound to a negatively charged Drude shell. We show that existing force fields that place all non-Coulomb forces on the Drude core and none on the shell inadvertently couple the dipole to non-Coulombic forces. This introduces errors where interactions with neutral particles can erroneously induce atomic polarization, leading to spurious polarizations in the absence of an electric field, exacerbating violations of equipartition in the employed Carr-Parinello scheme. A suitable symmetrization of the interaction potential that correctly splits the force between the Drude core and shell can correct this shortcoming, improving the stability and numerical performance of Drude oscillator-based simulations. The symmetrization procedure is straightforward and only requires the rescaling of a few force field parameters.

Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.

Accurate empirical force fields of lipid molecules are a critical component of molecular dynamics simulation studies aimed at investigating properties of monolayers, bilayers, micelles, vesicles, and liposomes, as well as heterogeneous systems, such as protein-membrane complexes, bacterial cell walls, and more. While the majority of lipid force field-based simulations have been performed using pairwise-additive nonpolarizable models, advances have been made in the development of the polarizable force field based on the classical Drude oscillator model. In the present study, we undertake further optimization of the Drude lipid force field, termed Drude2023, including improved treatment of the phosphate and glycerol linker region of PC and PE headgroups, additional optimization of the alkene group in monounsaturated lipids, and inclusion of long-range Lennard-Jones interactions using the particle-mesh Ewald method. Initial optimization targeted quantum mechanical (QM) data on small model compounds representative of the linker region. Subsequent optimization targeted QM data on larger model compounds, experimental data, and dihedral potentials of mean force from the CHARMM36 additive lipid force field using a parameter reweighting protocol. The use of both experimental and QM target data during the reweighting protocol is shown to produce physically reasonable parameters that reproduce a collection of experimental observables. Target data for optimization included surface area/lipid for DPPC, DSPC, DMPC, and DLPC bilayers and nuclear magnetic resonance (NMR) order parameters for DPPC bilayers. Validation data include prediction of membrane thickness, scattering form factors, electrostatic potential profiles, compressibility moduli, surface area per lipid, water permeability, NMR T1 relaxation times, diffusion constants, and monolayer surface tensions for a variety of saturated and unsaturated lipid mono- and bilayers. Overall, the agreement with experimental data is quite good, though the results are less satisfactory for the NMR T1 relaxation times for carbons near the ester groups. Notable improvements compared to the additive C36 force field were obtained for membrane dipole potentials, lipid diffusion coefficients, and water permeability with the exception of monounsaturated lipid bilayers. It is anticipated that the optimized polarizable Drude2023 force field will help generate more accurate molecular simulations of pure bilayers and heterogeneous systems containing membranes, advancing our understanding of the role of electronic polarization in these systems.

Modeling coarse-grained van der Waals interactions using dipole-coupled anisotropic quantum Drude oscillators.

The Quantum Drude Oscillator (QDO) model is a promising candidate for accurately calculating the van der Waals (vdW) interaction. Anisotropic QDO models have recently been used to represent quantum fluctuations of molecular fragments rather than that of single atoms. While this model promises accurate calculation of vdW energy, there is significant room for improvements, such as incorporating a proper fragmentation method, higher-order dispersion corrections, and so forth. The present work attempts to gauge dipole-dipole interactions' ability without fragmentation. A suitable anisotropic damping function is also introduced to work with anisotropic QDO. This revised model accurately predicts the binding energies of vdW complexes for most of the systems considered. This work indicates the limit of dipole approximation for an anisotropic QDO-based model.

Precise Design of VO2Thin Films for Smart Windows by Employing Thickness‐Dependent Refractive Index

Vanadium dioxide (VO2) is an adjustable refractive index material and has capability of behaving as semiconductor or conductor depending on its temperature. Such a condition makes it as a material which can be employed in fabricating thermochromic smart windows. The transmission characteristics of these type of windows strongly depend on the thickness of the film. Therefore, some calculations are required to optimize the VO2thickness. Since the refractive index of VO2thin film is thickness dependent, therefore, in calculating the transmission of light spectrum from VO2thin films, a unique refractive index cannot be utilized. Herein, using three theoretical models (Lorentz–Drude oscillator, Lorentz oscillator, and Tauc–Lorentz) and employing experimental results from previous reports, a collection of thickness‐dependent refractive indexes of VO2films is provided. More precise transmission can be achieved using this set of refractive index data in the calculations which agree with those of experiments. These results also make capable to determine optimized film thickness for any desired transmission performance. This method is useful for design of VO2‐based thermochromic smart windows.

Flexible Polarizable Water Model Parameterized via Gaussian Process Regression.

Water is one of the most common components in molecular dynamics (MD) simulations. Using Gaussian process regression for predicting the properties of a water model without the need of running a simulation whenever the parameters are changed, we obtained a flexible polarizable water model, named SWM4/Fw, that is able to reproduce many reference water properties. The added flexibility is critical for modeling chemical reactions in which chemical bonds can be stretched or even broken and for directly calculating vibrational spectra. In addition to being one of the few water models that are both flexible and polarizable, SWM4/Fw is also efficient thanks to the extended Lagrangian scheme with Drude oscillators. The overall accuracy is on par with or better than the related SWM4-NDP model.

Explicit Polarization in Coarse-Grained Simulations of Ionomer Melts

The structure and morphology of ionic aggregates in ionomer melts significantly influence their ion transport properties. Understanding the underlying mechanisms and relevant time scales of ion transport can facilitate design of viable ionomer materials as single-ion conductors for energy applications. Previous studies have characterized the ionic aggregate structure, morphology, and dynamics using non-polarizable coarse-grained molecular dynamics (CGMD) simulations. In this work, we examine the role of polarization in ionomer melts by explicitly incorporating Drude oscillators in CGMD simulations. We systematically study the structure and dynamics of pendant ionomers, focusing on the comparison to non-polarizable systems. Polarization within the ion clusters leads to less overall ion structuring. On the aggregate scale, less ion structuring yields smaller ionic aggregates. The extent to which the clusters are smaller delicately depends on the strength of the electrostatic interactions (the dielectric constant). Under certain conditions, we find that the time scale for free counterion diffusion does not depend on the morphology, unlike that in a non-polarizable model.

Water Thermodynamic Behavior Under Influence of Electric Field: A Molecular Dynamics Study

Abstract Water phase-change is of importance to many applications including energy conversion, thermal management of electronics, and medical therapies. Augmenting the rate of phase-change by application of an electric field is of interest in many situations and may lead to increased effectiveness of energy transfer. Thus, it is important to develop a better understanding of the effect of an electric field on the thermodynamic properties of water. In this work, molecular dynamics (MD) was utilized to assess two distinct water models, the TIP4P-Ew and the SWM4-NDP, for predicting the effect of an electric field on the density and the enthalpy of vaporization of water. Both water models possess rigid molecular geometry. However, the SWM4-NDP model has a negatively charged Drude particle (the “NDP”) attached to the oxygen site in the water molecule, making the SWM4-NDP model polarizable. The objective is to understand if the polarizability of the water model has a significant effect when predicting the two properties of interest. Applying an electric field in MD simulations with each water model resulted in increased values for both the density and enthalpy of vaporization. The magnitude of these increases is comparable between water models and grows with applied field strength. Corresponding electrostriction pressure attributed to the applied field is well below values predicted by analytical models.

Heterogeneous hydration patterns of G-quadruplex DNA

G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although extensively studied through various experimental and computational methods, hydration patterns near DNA remain under debate due to the chemically and topologically heterogeneous nature of the exposed surface. In this work, we employed all-atom molecular dynamics (MD) simulation to study the hydration patterns of GQ DNA. The Drude oscillator model was used in MD simulation as a computationally efficient method for modeling electronic polarization in DNA ion solutions. Hydration structure was analyzed in terms of radial distribution functions and high-density three-dimensional hydration sites. Analysis of hydration dynamics focused on self-diffusion rates and orientation time correlation at different structural regions of GQ DNA. The results show highly heterogeneous hydration patterns in both structure and dynamics; for example, there are several insular high-density sites in the inner channel, and ‘spine of water’ in the groove. For water inside the loop, anomalous diffusion is present over a long time scale, but for water around the phosphate group and groove, diffusion becomes normal after ∼ 30 ps. These essentially correspond to deeply buried structural water and strong interaction with DNA, respectively.