Atomic Polarizabilities Research Articles

Quantum friction between metals in the hydrodynamic regime

In this work, we study the phenomenon of quantum friction in a system consisting on an atom moving at a constant speed parallel to a metallic plate. We use a hydrodynamic model to describe the degrees of freedom of a clean metal without internal dissipation. We model the polarizable atom as a two-level system with a unique ($l=0$) ground state and a threefold degenerate ($l=1$) excited state. We show that a quantum frictional force is present even in the absence of intrinsic damping in the metal, but that there is a threshold in the relative velocity that gives rise to such a force. In particular, we find that for friction to occur, the atom must move at a velocity larger than the effective speed of sound in the material, a condition that can be reached near empty or filled bands, where the Fermi velocity (which is proportional to the sound speed) becomes low. We provide analytical arguments to show that this result holds at all orders in perturbation theory.

Measurement of dynamic atomic polarizabilities of Al at 19 wavelengths from 420 nm to 680 nm in electrical exploding wire experiments.

The dynamic polarizabilities of Al atom at 19 wavelengths from 420 nm to 680 nm are measured experimentally for the first time. A 15 µm diameter Al wire is heated to the gas/ microdrop stage using a 3 kA, 25 ns pulsed current, and the energy deposition when the resistive voltage reaches its peak is 4.7 eV·atom-1, which is higher than the atomization enthalpy of Al but much lower than its first ionization potential. Two laser interferometric images of the Al gas are obtained simultaneously using a 532 nm laser and an optical parametric oscillator laser. Then an integrated phase method is used to reconstruct the Al atomic linear density distribution based on the known atomic polarizability at 532 nm, which acts as a bridge between the two interferograms to obtain the relative atomic polarizability value at a specific wavelength with respect to the value at 532 nm. The measured dynamic polarizability of Al atom decreases from 13.5×10-24 cm3 to 9.4×10-24 cm3 as the wavelength increases from 420 nm to 680 nm with a measurement error of approximately ±10%. The experimental result fits well with an uncoupled Hartree-Fock approximation, and the reconstructed static polarizability of 8.13 ± 0.79×10-24 cm3 is well matched with reference measurement results.

Laser measurements of static and dynamic dipole polarizability for 11 metal atoms using fast exploding wires in vacuum and integrated-phase technique

The rapid electrical explosion of thin metal wires in a vacuum can completely vaporize the wire and form a fast-expanding gas cylinder of metal atoms. Thin metal wires 12.7 μm in diameter made of W, Mo, Pt, Pd, Ni, Cu, Au, and Al completely evaporated during the first ∼10 ns under the action of a fast-rising current of ∼1 kA/ns. Laser interferometry and the integrated phase technique were used to reconstruct the dynamic atomic polarizability for fully vaporized thin metal wires at 532 and 1064 nm wavelength, calculate the static atomic polarizability, the first dipole-allowed electronic transition energy, and transition wavelengths, and compare our reconstructions with available tabulated values.

Electric dipole moments and static dipole polarizabilities of alkali-metal–alkaline-earth-metal molecules: Nonrelativistic versus relativistic coupled-cluster-theory analysis

We analyze the electric dipole moments (PDMs) and static electric dipole polarizabilities of the alkali--alkaline-earth (Alk-AlkE) dimers by employing finite-field coupled-cluster methods, both in the frameworks of non-relativistic and four-component spinfree relativistic theory. In order to carry out comparative analyses rigorously, we consider those Alk-AlkE molecules made out of the lightest to the medium-heavy constituent atoms (Alk: Li to Rb and AlkE: Be through Sr). We present behaviour of electron correlation effects as well as relativistic effects with the size of the molecules. Uncertainties to the above quantities of the investigated Alk-AlkE molecules are inferred by analyzing our results from different form of Hamiltonian, basis set, and perturbative parameter in a few representative molecules. We have also provided empirical relations by connecting average polarizabilities of the Alk-AlkE molecules with their PDMs, and atomic numbers and polarizabilities of the corresponding Alk and AlKE atoms, which can be used to roughly estimate the average polarizabilities of other heavier Alk-AlkE molecules. We finally give our recommended results, and compare them with the literature values.

A Unified Approach to Derive Atomic Partial Charges and Polarizabilities of Ionic Liquids.

We propose a unified approach to fit simultaneously a set of atomic partial charges and polarizabilities of the polarizable model against the ab initio electrostatic potential (ESP) and polarizability. The polarizable model is represented with interactive atomic dipoles with distance-dependent attenuation. For the polarizable model employed in this study, the internal electric field on the polarization sites is fully turned on, and thus allows self-induced dipoles, which persist even for an isolated molecule/ion. By such treatment, the contribution of ESP stems not only from the partial charges but also from the self-induced dipoles, and the atomic partial charges and polarizabilities can be fitted simultaneously against ESP in a unified manner. The fitting with 1-ethyl-3-methylimidazolium (EMIM+) and nitrate (NO3-), a prototypical organic cation and inorganic anion, respectively, that can form ionic liquid, demonstrates that allowance of the self-induced dipoles gives much better fitness. Moreover, test on the total dipole of an EMIM+/NO3- ion pair shows that the agreement with the ab initio dipole is also much improved for the polarizable model, which highlights the importance of the polarization effects of ionic liquids.

Potential risk resulting from the influence of static magnetic field upon living organisms. Numerically-simulated effects of the static magnetic field upon carbohydrates

Background: Recognising effects of static magnetic field (SMF) of varying flux density on flora and fauna is attempted. For this purpose, the influence of SMF upon molecules ofα- andβ-D-glucose,α- andβ-D-galactose,α- andβ-fructopyranoses,α- andβ-fructofuranoses andα- andβ-D-xylofuranoses andαandβ-D-xylopyranoses is studied.Methods: Computations of the effect of static magnetic field (SMF) of 0.0, 0.1, 1, 10 and 100 AFU (1 AFU > 1000 T) flux density were performed in silico for SMF changes distribution of the electron density in these molecules.Hyper-Chem 8.0 software was used together with the AM1 method for optimisation of the conformation of the molecules of monosaccharides under study. Then polarisability, charge distribution, potential and dipole moment for molecules placed in SMF were calculated involving DFT 3-21G method.Results: Application of SMF induced polarisability of electrons, atoms and dipoles, the latter resulting in eventual re-orientation of the molecules along the applied field of the molecules and the electron density redistribution at particular atoms. Increase in the field strength generated mostly irregular changes of the electron densities at particular atoms of the molecules as well as polarisabilities. Energy of these molecules and their dipole moments also varied with the SMF flux density applied.Conclusions: Saccharides present in the living organisms may participate in the response of the living organisms to SMF affecting metabolism of the molecules in the body fluids by fitting molecules to the enzymes. Structural changes of saccharide components of the cell membranes can influence the membrane permeability.

Electric Properties of Photochromic Molecules Physisorbed on Silver and Copper Nanoparticles.

This paper investigates the electric properties of the photochromic dihydroazulene/vinylheptafulvene system as it is physisorbed onto silver and copper nanoparticles. Our focus is on how the polarizability and hyperpolarizability of the dihydroazulene, s-cis-vinylheptafulvene, and s-trans-vinylheptafulvene molecules depend on molecular orientation with respect to the nanoparticles, the molecule-cluster separation, and the type of nanoparticle. The computational approach utilizes a combined quantum mechanical/molecular mechanical method in which the molecules are treated quantum mechanically while the nanoparticles are treated with a simpler classical method. The molecules are described with density functional theory. The electric properties are calculated using response theory utilizing the long-range-corrected functional CAM-B3LYP and the correlation consistent basis set aug-cc-pVDZ. The atoms of the nanoparticles are represented using atomic polarizabilities. The interactions between the nanoparticles and the molecular systems are calculated using a polarizable embedding scheme after which the molecular properties are calculated with time-dependent density functional theory. The results show that the electric properties are indeed affected by the presence of the nanoparticles. It is also clear that it is the hyperpolarizabilities that change the most while the polarizabilities are less affected. Furthermore, the influence of the nanoparticles on the molecules depends heavily on the relative molecular orientation with respect to the nanoparticles and molecular conformation. Finally, it is observed that a copper nanoparticle has a larger influence on the molecular systems than a silver nanoparticle.

In silico approach for potential antimicrobial agents through antiviral, molecular docking, molecular dynamics, pharmacokinetic and bioactivity predictions of galactopyranoside derivatives

Carbohydrates derivatives played an important and vital role in a large part to design new potential drug against various pathogens, in medicinal chemistry. Also, monosaccharide derivatives are very useful in biological chemistry because monosaccharide binding agents were shown to possess antiviral, antibacterial, and antifungal activity towards HIV, Dengue coronaviruses, and many members of the family Enterobacteriaceae, including strains of Escherichia coli, Salmonella typhimurium, Klebsiella pneumoniae, Shigella flexneri, and Enterobacter aerogenes. The present study was therefore interesting in identifying the binding affinity of a series of monosaccharides previously synthesized through their physicochemical and pharmacokinetic properties. These monosaccharides are derivatives of methyl-β-D-galactopyranoside (MGP) coupled to the protein deacetoxycephalosporin C synthase (DAOCS) of Streptomyces clavuligerus (1RXF). Molecular docking study against DAOCS proteins (PDB ID: 1RXF) was performed assess the antimicrobial activities of these derivatives along with antiviral prediction. The results of molecular docking studies showed that derivatives 8 and 10 both presented the highest score (-7.2 kcal/mol), reflecting their good binding affinity toward the active pocket of the pathogen S. clavuligerus (1RXF). They are found to be potent antimicrobial agents. These findings were further validated in dynamics (200 ns) milieu and intermolecular stability was evaluated via highly acceptable Molecular Mechanics Poisson-Boltzmann Surface Area (MMPB)/Molecular Mechanics/Generalized Born Surface Area (GBSA) binding free energies estimation methods. The dynamics of the complexes are highly stable with the strengthening of docked interactions as highlighted by MMPB/GBSA method (net binding energy < −40 kcal/mol). Density functional theory (DFT) calculations were carried out on the derivatives of MGP in order to determine the partial atomic charges, electronic energies, enthalpies, entropies and polarizability, at the B3LYP/3-21G level. The in silico ADMET prediction carried out provided access to the bioactivity and toxicity parameters which established that most of the different ligands designed are safe to use as drugs. This in silico study provided an overall view of the possible pharmacological and therapeutic profile of MGP derivatives. It therefore, paved the way for the discovery of promising next-generation drugs against pathogenic microbes.

Azide–Alkyne Interactions: A Crucial Attractive Force for Their Preorganization for Topochemical Cycloaddition Reaction

A new class of attractive intermolecular interaction between azide and ethynyl structural entities in a wide range of molecular crystals is reported. This interaction was systematically evaluated by using 11 geometrically different structural motifs that are preorganized to direct a solid-state topochemical azide-alkyne cycloaddition (TAAC) reaction. The supramolecular features of the azide-alkyne interaction were mapped by various crystallographic and quantum chemical approaches. Topological analysis shows the noticeable participation of electron density in the azide⋅⋅⋅alkyne interactions. Interestingly, reorientation of the atomic polarizabilities in vicinal azide and alkyne groups upon interaction in crystals favors soft orbital-guided TAAC reactions. Moreover, various solid-state and gas-phase energy decomposition methods of individual azide⋅⋅⋅alkyne interactions summarize that the strength (varies from -5.7 to -30.1 kJ mol-1 ) is primarily guided by the dispersion forces with a influencing contribution from the electrostatics.

Mutually guided light and particle beam propagation

The polarizability of atoms and molecules gives rise to optical forces that trap particles and a refractive index that guides light beams, potentially leading to a self-guided laser and particle beam propagation. In this paper, the mutual interactions between an expanding particle beam and a diffracting light beam are investigated using an axisymmetric particle-light coupled simulation. The nonlinear coupling between particles and photons is dependent on the particle beam radius, particle density, particle velocity and temperature, polarizability, light beam waist, light frequency (with respect to the resonance frequency), and light intensity. The computational results show that the maximum propagation distance is achieved when the waveguiding effect is optimized to single-mode operation. The application of the coupled beam propagation as a space propulsion system is discussed.

On the generation of MCs+ ions in SIMS with Cs+ primary beams

The formation of MCs+ secondary ions in SIMS operated with Cs+ ion beams is discussed on the basis of a well‐confirmed quadratic dependence of MCs+ yields on the atomic polarizabilities of elements M contained in semiconductor samples. This behavior is understood by the generation of a dipole induced in M by the positive charge of a neighboring Cs+ projectile and the mutual induction of a dipole in Cs+, both dipoles depending on the atomic polarizability of M. An evaluation of the dipole–dipole interaction energy indicates that MCs+ ions generated at the target are emitted according to the direct emission model (DEM). This mechanism is in contrast with an association model where constituents of MCs+ are assumed to combine after their independent sputter emission.

Does Explicit Polarizability Improve Molecular Dynamics Predictions of Glass Transition Temperatures of Ionic Liquids?

Molecular dynamics simulations are used for predictions of the glass transition temperatures for a test set of five aprotic ionic liquids. Glass transitions are localized with the trend-shift method, analyzing volumetric and transport properties of bulk amorphous phases. A classical nonpolarizable all-atom OPLS force-field model developed by Canongia Lopes and Pádua (CL&P) is employed as a starting level of theory for all calculations. Alternative approaches of charge scaling and the Drude oscillator model, accounting for atomic polarizability either implicitly or explicitly, respectively, are used to investigate the sensitivity of the glass transition temperatures to induction effects. The former nonpolarizable model overestimates the glass transition temperature by tens of Kelvins (37 K on average). The charge-scaling technique yields a significant improvement, and the best estimations were achieved using polarizable simulations with the Drude model, which yielded an average deviation of 11 K. Although the volumetric data usually exhibit a lesser trend shift upon vitrification, their lower statistical uncertainty enables to predict the glass transition temperature with lower uncertainty than the ionic self-diffusivities, the temperature dependence of which is usually more scattered. Additional analyses of the simulated data were also performed, revealing that the Drude model predicts lower densities for most subcooled liquids but higher densities for the glasses than the original CL&P, and that the Drude model also invokes some longer-range organization of the subcooled liquid, greatly impacting the temperature trend of ionic self-diffusivities in the low-temperature region.

Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field.

The Drude polarizable force field (FF) captures electronic polarization effects via auxiliary Drude particles that are attached to non-hydrogen atoms, distinguishing it from commonly used additive FFs that rely on fixed charges. The Drude FF currently includes parameters for biomolecules such as proteins, nucleic acids, lipids, and carbohydrates and small-molecule representative of those classes of molecules as well as a range of atomic ions. Extension of the Drude FF to novel small druglike molecules is challenging as it requires the assignment of partial charges, atomic polarizabilities, and Thole scaling factors. In the present article, deep neural network (DNN) models are trained on quantum mechanical (QM)-based partial charges and atomic polarizabilities along with Thole scale factors trained to target QM molecular dipole moments and polarizabilities. Training of the DNN model used a collection of 39 421 molecules with molecular weights up to 200 Da and containing H, C, N, O, P, S, F, Cl, Br, or I atoms. The DNN model utilizes bond connectivity, including 1,2, 1,3, 1,4, and 1,5 terms and distances of Drude FF atom types as the feature vector to build the model, allowing it to capture both local and nonlocal effects in the molecules. Novel methods have been developed to determine restrained electrostatic potential (RESP) charges on atoms and external points representing lone pairs and to determine Thole scale factors, which have no QM analogue. A penalty scheme is devised as a performance predictor of the trained model. Validation studies show that these DNN models can precisely predict molecular dipole and polarizabilities of Food and Drug Administration (FDA)-approved drugs compared to reference MP2 calculations. The availability of the DNN model allowing for the rapid estimation of the Drude electrostatic parameters will facilitate its applicability to a wider range of molecular species.

Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.

Molecular dynamics (MD) simulations play a crucial role in modeling biomolecular systems in which the electrostatic interactions are critical in dictating the structural and dynamical properties. Thus, the treatment of the electrostatic interactions defined in the underlying force field (FF) strongly affects the simulation accuracy. Most FFs use fixed partial atomic charges to include electrostatic interactions, and therefore lack the electronic polarization response, representing an intrinsic limitation. To address this limitation, polarizable FFs have been developed that treat atomic polarizabilities explicitly. Here we present the application of the all-atom polarizable (Drude) and non-polarizable (CHARMM) nucleic acid FFs in RNA hairpin systems to investigate the impact of polarization on structural properties, dipole moment distributions, and cation interactions. Results show that the presence of polarizability in the FF significantly improves the stabilization of RNA hairpin structure. As expected, the distributions of dipole moments show more fluctuations when simulated using the polarizable FF, with the variation in dipoles contributing to the stabilization of the structures of the loop regions of the RNAs. Contact map analyses between the bases and cations show that the variation of the ion distribution around the entire hairpin is larger for the polarizable FF and the cations occupy the outer hydration shell to a greater extent. The presented results indicate the importance of the explicit treatment of electronic polarizability in molecular simulations of RNA, including in non-canonical regions.

The Computational Study, 3D-QSAR, and Molecular Docking Study of 2-Amino 5-Methyl Pyridine

The indeed optimized structure of the 2-Amino 5-Methyl Pyridine (2A5MP) and its minimum energies were analyzed by using B3LYP functional with B3LYP/6-311++G (d, p) basis set. The first hyperpolarizability (β), polarizability (α), and dipole moment (μ) of the compound were computed and the results were reported. The Mulliken charges, atomic polarizability tensor (APT) charges and HOMO-LUMO energy difference were calculated. This energy difference illustrates the properties of optical polarizability, chemical hardness/softness, and kinetic stability/reactivity of a molecule. NBO analysis was executed to know the transfer of electrons within the molecule and molecular electrostatic potential (MEP) analysis was also performed. The docking procedure was accomplished between 2- amino 5-methyl pyridine and rigid protein receptors. Druglikeness principles are based on the rules of Lipinski and Veber appraise that the title molecule had the ideal physicochemical and pharmacokinetic properties to be a good drug candidate orally. The docking studies were carried out and analyzed in order to understand the binding mode of the titled compound and it was found to have a binding energy of −3.32 kcal/mol.

Motion-induced energy shifts of a multilevel atom in a black-body radiation field

We investigate the influence of atomic uniform motion on radiative energy shifts of a multilevel atom when it interacts with black-body radiation. Our analysis reveals that the atomic energy shifts depend crucially on three factors: the temperature of black-body thermal radiation, atomic velocity, and atomic polarizability. In the low-temperature limit, the presence of atomic uniform motion always enhances the effect of the thermal field on the atomic energy shifts. However, in the high-temperature limit, the atomic uniform motion enhances the effect of the thermal field for an atom polarizable perpendicular to the atomic velocity but weakens it for an atom polarizable parallel to the atomic velocity. Our work indicates that the physical properties of atom–field coupling systems can in principle be regulated and controlled by the combined action of the thermal field and the atomic uniform motion.

Study of Differential Cross-Section and S-Matrix Using Volkov Function and Taylor Series Expansion for Elastic Scattering

This paper deals with S-matrix, born first approximation, amplitude, and differential cross-section (DCS), using Volkov function and Taylor series expansion in laser field, scattering. Equation (30) copes-with DCS and Equation (36) deals with S-matrix, with different parameters, moreover, both equations contain real and imaginary parts. The DCS increases with increasing angle and polarizabilities, constant with dipole distance for both emission and absorption of single-photon. The DCS for both emission and absorption is responded to low incidence energy (30 eV - 60 eV) and photon energy (15 eV) while at high energy only emission and absorption are responded for DCS. The DCS between absorption and emission of a photon with angle variation, dipole distance, and atomic polarizabilities was found 1.098 a.u.2 and at high incidence, energies were found 0.1 a.u.2.

Атомные наноструктурные системы с отрицательной экстинкцией

This article proves the fundamental possibility of amplifying light by a system of indistinguishable atoms, taking into account the delayed dipole-dipole interaction in the field of external radiation. It is shown that the amplification of light occurs from an antisymmetric quantum state of a pair of identical atoms, one of which is in an excited state. A formula is obtained for the polarizability of atoms in the ground state, the dispersion dependence of which contains an inflection point separating the wavelength regions with positive and negative dispersion. In the region of negative dispersion, the extinction cross section of an atomic system is negative, that is, this system becomes a system that amplifies light.

High dielectric constant and high breakdown strength polyimide via tin complexation of the polyamide acid precursor.

Polymer dielectrics with ultra-high charge–discharge rates are significant for advanced electrical and electronic systems. Despite the fact that polymers possess high breakdown strength, the low dielectric constant (k) of polymers gives rise to low energy densities. Incorporating metal into polyimides (PI) at the polyamic acid (PAA) precursor stage of the synthetic process is a cheap and versatile way to improve the dielectric constant of the hybrid system while maintaining a high breakdown strength. Here, we explore inclusion of different percentages of Sn as a coordinated complex in a polyimide matrix to achieve metal homogeneity within the dielectric film to boost dielectric constant. Sn–O bonds with high atomic polarizability are intended to enhance the ionic polarization without sacrificing bandgap, a measurable property of the material to assess intrinsic breakdown strength. Enhancements of k from ca. 3.7 to 5.7 were achieved in going from the pure PI film to films containing 10 mol% tin.

Knowledge-Based Atomic Polarizabilities Used to Model Circular Dichroism Spectra of Proteins.

We present a model of circular dichroism for proteins, which is mainly based on both the classical theory of optical activity and a series of effective atomic polarizabilities. Such polarizabilities are extracted from the analysis of a set of synchrotron radiation circular dichroism spectra and their corresponding three-dimensional structures from the Protein Data Bank. Each modeled spectrum is obtained from the protein atomic coordinates and the identification of its secondary structure elements. The resulting spectra are in good agreement with additional experimental data and also with the predictions of some other models. Among them, only our approach is able to describe the effect of d-amino acids. Moreover, our model is also utilized to evaluate protein reconstructions as well as structural changes.