Atomic Polarizabilities Research Articles

Role of Environmental Dynamic Polarizability in Static Excited State Properties of Embedded Molecular Systems: Application to Disordered Fluorographene Systems

We present an extension of the standard polarizable quantum mechanic/molecular mechanics (QM/MM) approach for treating environmental effects on excited state properties of embedded systems. A quantum polarizable atom model is derived from a full quantum description of the environment using perturbation theory for the system-environment coupling. Our model provides a more general description of the environment, including frequency-dependent atomic polarizabilities, without the loss of computational simplicity of the QM/MM approach. The classical polarizable atom description, used in the polarizable QM/MM approach, can be obtained as a limiting case of the present model. This result enables us to pinpoint approximations and assumptions about the system inherent to a classical polarizable atom description of the environment. We apply our method to fluorographene (FG)-based systems to investigate the effects of the FG sheet on excited state properties of impurities on the FG surface. The comparison to full quantum chemistry calculations and to the standard polarizable QM/MM approach on disordered fluorographene clusters reveals the importance of the frequency dependence of atomic polarizabilities for a proper treatment of the effects of the environment on both the transition energy shifts and the interaction energies.

Accurate Metal-Imidazole Interactions.

Modeling the interaction between a metal ion and small molecules can provide pivotal information to bridge and close the gap between two types of simulations: metal ions in water and metal ions in metalloproteins. As previously established, the 12-6-4 Lennard-Jones (LJ)-type nonbonded model, because of its ability to account for the induced dipole effect, has been highly successful in simulating metal ion systems. Using the potential of mean force (PMF) method, the polarizability of the metal-chelating nitrogen from two types of imidazole molecules, delta nitrogen protonated (HID) and epsilon nitrogen protonated (HIE), has been parametrized against experiment for 11 metals (Ag(I), Ca(II), Cd(II), Co(II), Cu(I), Cu(II), Fe(II), Mg(II), Mn(II), Ni(II), and Zn(II)) in conjunction with three commonly used water models (TIP3P, SPC/E, and OPC). We show that the standard 12-6 and unmodified 12-6-4 models are not able to accurately model these interactions and, indeed, predict that the complex should be unstable. The resultant parameters further establish the flexibility and the reliability of the 12-6-4 LJ-type nonbonded model, which can correctly describe three-component interactions between a metal, ligand, and solvent by simply tuning the polarizability of the chelating atom. Also, the transferability of this model was tested, showing the capability of describing metal-ligand interactions in various environments.

Analysis of Quantitative Structure-Activity Relationship (QSAR) Of 1,8-Napthalymide-4-Aminoquinoline Derivatives as Antimalarial Compounds

QSAR analysis from derivative compounds of 1,8-naphthalimide-4-aminoquinoline has been carried out with the aim of knowing the quantitative relationship between structure and activity based on the log IC50 value. The modelling was made with two dimensions and geometric optimization is carried out. The AM1 semi-empirical method was used to optimize the geometry of the total energy of 25 compounds. The descriptors in the QSAR calculation were dipole moment, atomic net charge, ELUMO, EHOMO, SAG, SAA, hydration energy, polarizability, and log P. The descriptors were used to find quantitative equations of the relationship between the structure and antimalarial activity.

Synthesis, Antiproliferative Evaluation and QSAR Analysis of Novel Halogen- and Amidino-Substituted Benzothiazoles and Benzimidazoles.

Syntheses of 6-halogen-substituted benzothiazoles were performed by condensation of 4-hydroxybenzaldehydes and 2-aminotiophenoles and subsequent O-alkylation with appropriate halides, whereas 6-amidino-substituted benzothiazoles were synthesized by condensation of 5-amidino-2-aminothiophenoles and corresponding benzaldehydes. While most of the compounds from non-substituted and halogen-substituted benzothiazole series showed marginal antiproliferative activity on tested tumor cell lines, amidino benzazoles exhibited stronger inhibitory activity. Generally, imidazolyl benzothiazoles showed pronounced and nonselective activity, with the exception of 36c which had a strong inhibitory effect on HuT78 cells (IC50 = 1.6 µM) without adverse cytotoxicity on normal BJ cells (IC50 >100 µM). Compared to benzothiazoles, benzimidazole structural analogs 45a-45c and 46c containing the 1,2,3-triazole ring exhibited pronounced and selective antiproliferative activity against HuT78 cells with IC50 < 10 µM. Moreover, compounds 45c and 46c containing the methoxy group at the phenoxy unit were not toxic to normal BJ cells. Of all the tested compounds, benzimidazole 45a with the unsubstituted phenoxy central core showed the most pronounced cell growth inhibition on THP1 cells in the nanomolar range (IC50 = 0.8 µM; SI = 70). QSAR models of antiproliferative activity for benzazoles on T-cell lymphoma (HuT78) and non-tumor MDCK-1 cells elucidated the effects of the substituents at position 6 of benzazoles, demonstrating their dependence on the topological and spatial distribution of atomic mass, polarizability, and van der Waals volumes. A notable cell cycle perturbation with higher accumulation of cells in the G2/M phase, and a significant cell increase in subG0/G1 phase were found in HuT78 cells treated with 36c, 42c, 45a-45c and 46c. Apoptotic morphological changes, an externalization of phosphatidylserine, and changes in the mitochondrial membrane potential of treated cells were observed as well.

Polarizable Molecular Block Model: Toward the Development of an Induced Dipole Force Field for DNA.

For flexible and highly ionized macromolecules such as DNA, it is important to correctly evaluate the intramolecular polarization in an induced dipole force field. In a proposed polarizable molecular block (PMB) model, a large molecule is divided into several molecular blocks. The atomic charges of the blocks are optimized by using the respective electrostatic potentials (ESPs) on the molecular surface. By using the capped hydrogen removal operation, the total charge of the blocks is controlled exactly to have an integer charge. The atomic polarizabilities of the blocks are optimized by using the respective polarized one-electron potentials that are the differences between ESPs with and without an external test charge. Induced dipole-charge interactions between the blocks are all included, but those interactions within the blocks are strictly excluded. All dipole-dipole interactions are included, but the damping functions are applied to the close dipole-dipole pairs. Several types of damping (simple scaling, exponential, linear, and Gaussian) are evaluated. The validity of the PMB model was verified by using trinucleotide duplexes which have A-, B-, and Z-DNA forms. The reference energies of trinucleotide duplexes including counterions (GGT3Na-ACC3Na, GAC3Na-GTC3Na, and GCG3Na-CGC3Na) are calculated using ωB97XD/aug-cc-pVDZ. All damping types reproduced well the reference interaction energies, dipole moments, and ESPs. Among them, the simple scaling with strong attenuation to 1-2 atomic pairs showed the highest stability against the polarization catastrophe. This study shows that it is possible to develop a high-quality polarizable force field by treating the intramolecular polarization on a block-by-block basis.

Abnormalities of the Halogen Bonds in the Complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I).

In this work, the hydrogen bonds and halogen bonds in the complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I) have been studied by quantum chemical calculations. We found three interesting abnormalities regarding the interactions. Firstly, the strength of halogen bonds increases in the order of IF < BrF < ClF < F2. Secondly, the halogen bonds formed by F2 are very strong, with an interaction energy in the range between −199.8 and −233.1 kJ/mol. Thirdly, all the halogen bonds are stronger than the hydrogen bonds in the systems we examined. All these results are against the general understanding of halogen bonds. These apparent abnormal properties are reconciled with the high polarizability of the Te atom and the strong inducing effect of F on the Te atom of Y2CTe. These findings provide a new perspective on halogen bonds. Additionally, we also proposed bonding distance-based methods to compare the strength of halogen/hydrogen bonds formed between different donor atoms and the same acceptor atom.

MoS2-functionalized attapulgite hybrid toward high-performance thickener of lubricating grease

An important prerequisite for developing high-performance industrial lubricating grease is to regulate the composition and structure of thickener for obtaining lubrication function. Herein, MoS2-grafted attapulgite (ATP) hybrid as grease thickener was prepared by one-step hydrothermal method. The polarizable Mo atoms were coupled with the tetrahedral structure of ATP matrix to yield MoS2-functionalized ATP (ATP/MoS2) hybrid. The regulated-grease using ATP/MoS2 as thickener in poly-alpha-olefin (PAO40) oil significantly reduces the friction (31.5%) and wear (37.5%) due to the synergy of as-prepared ATP/MoS2 thickener with superior thickening and lubrication function. The achievement of superior tribological properties mainly depends on the interlayer slip of even-distributed MoS2 and tribo-chemical film. MoS2-functionalized ATP might guide the development of a novel nano-thickener for high-performance lubricating grease.

A building-block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium.

Since atomic or functional-group properties in the bulk are generally not available from experimental methods, computational approaches based on partitioning schemes have emerged as a rapid yet accurate pathway to estimate the materials behavior from chemically meaningful building blocks. Among several applications, a comprehensive and systematically built database of atomic or group polarizabilities and related opto-electronic quantities would be very useful not only to envisage linear or non-linear optical properties of biomacromolecules but also to improve the accuracy of classical force fields devoted to simulate biochemical processes. In this work, we propose the first entries of such database that contains distributed polarizabilities and dipole moments extracted from fragments of peptides. Twenty three prototypical conformers of the dipeptides alanine-alanine and glycine-glycine were used to extract functional groups such as CH2 , CHCH3 , NH2 , COOH, CONH, thus allowing construction of a diversity of chemically relevant environments. To evaluate the accuracy of our database, reconstructed properties of larger peptides containing up to six residues of alanine and glycine were tested against density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory. The procedure is particularly accurate for the diagonal components of the polarizability tensor with errors up to 15%. In order to include solvent effects explicitly, the peptides were also surrounded by a box of water molecules whose distribution was optimized using the CHARMM force field. Solvent effects introduced by a classical dipole-dipole interaction model were compared to those obtained from polarizable-continuum model calculations.

Observation of quantum capture in an ion-molecule reaction

In 1954, Vogt and Wannier (Phys. Rev. 95, 1190) predicted that the capture rate of a polarizable neutral atom or molecule by an ion should increase by a factor of two compared to the classical Langevin rate as the collision energy approaches zero. This prediction has not been verified experimentally. The H$_2^+$ + H$_2$ reaction is ideally suited to observe this effect, because the small reduced mass makes quantum effects related to s-wave scattering observable at higher collision energies than in other systems. Moreover, the reaction rate for this barrierless, strongly exothermic reaction follows the classical Langevin capture model down to cold-collision conditions (about $k_\mathrm{B} \cdot~1\,\mathrm{K}$) and is not affected by short-range interactions. Below this temperature, a strong enhancement of the reaction rate resulting from charge--quadrupole interaction between H$_2^+$ and ground-state ortho H$_2$ ($J=1$) was observed. Here we present an experimental study of the reaction of H$_2^+$ and para H$_2$ ($J=0$), which has no dipole and no quadrupole moments, at collision energies below $k_\mathrm{B}\cdot 1\,\mathrm{K}$. We observe an enhancement at the lowest collision energies which is attributed to the quantum enhancement predicted by Vogt and Wannier. Measurements of the reaction of HD$^+$ with HD support this conclusion.

Reconciliation of the Theoretical and Experimental Value of the Static Electric Polarizability of the Aluminum Atom

Reconciliation of the Theoretical and Experimental Value of the Static Electric Polarizability of the Aluminum Atom

Rayleigh scattering from hydrogen atoms including resonances and high photon energies

The nonrelativistic cross section from Rayleigh scattering by hydrogen atoms in the ground state was calculated over a wide range of photon energies (&lt;0.8 keV). Evaluations were performed in terms of the real and imaginary components of the atomic polarizability. The sum over intermediate states that characterizes this second-order radiative process was performed using exact analytic expressions for oscillator strengths of bound and continuum states. Damping terms associated with the finite lifetimes of excited states and their splitting into two fine-structure levels (p1/2 and p3/2) are taken into account in resonance cross sections. Fitting formulas required for cross-section evaluation are presented for incident photon energy (i) redward of the first resonance (Lyman-α1/2), (ii) in the spectral region corresponding to resonances (for an arbitrary number of them), and (iii) above the ionization threshold.

A CRYSTAL-based parameterization of carbon atom dynamic polarizabilities to compute optical properties of curved carbonaceous nanostructures

The radiative forcing of dust particles in Earth atmosphere is still poorly characterized. A better estimation of the absorption cross section of dust particles in the UV-visible part of the spectrum is thus needed. Among the methods used for this purpose, the Atomic Point Dipole Interaction model has the distinctive advantage of being sensitive to the atomistic geometry of the particle and to the chemical functions it contains. However, this requires an adequate parameterization of the atomic polarizabilities for all the atomic species forming the particle, over the UV-visible spectrum. In this paper, we illustrate how new methodological improvements based on quantum chemistry, allow taking into account the curvature of the carbon network in the parametrization of the carbon atomic polarizabilities, using the C $$_{60}$$ molecule to fit the adequate set of parameters. We thus show how this leads to significant differences in the computed curves of the absorption cross section of pure carbonaceous nanoparticles as a function of the frequency, with respect to calculations performed using parameters issued from graphite.

Cohesion energy simulation of inorganic layered alkaline-earth fluorohalides

Within the framework of an interionic potential model, electrostatic and repulsive energies, lattice self-potentials for distinct ions, and the Madelung constant were calculated for several technologically important layered alkaline-earth fluorohalide scintillators belonging to the matlockite family and crystallizing with the PbFCl-type structure. The Coulombic term was computed using the conventional Ewald method, where the formulas were adjusted to optimize the computer calculation, and the overlap repulsive term was computed by means of an empirical approach based on the compressible ionic theory. The dispersive contribution was quantified using well-known formulations, and the polarization contribution was determined purely by geometric considerations based on both the size and anisotropic coordination of the highly polarizable halogen atom. In general, the obtained results were found to be in close agreement with the available data, except for the contribution of short-range interactions in the lattice. A quantitative explanation has been proposed to elucidate the differences detected. It was pointed out that the structural stability of these lamellar structures can be understood in terms of the anisotropic coordination of halogen anions, especially the high coordination of metal cations combined with their sizes. Our calculations led to an accurate evaluation of the cohesive energy, which, to the best of our knowledge, has never been measured before. Finally, the corresponding results will be useful for a better understanding of the chemical bonds and structural behavior of PbFCl-type compounds at high pressures.

Classical Exchange Polarization: An Anisotropic Variable Polarizability Model.

Polarizability, or the tendency of the electron distribution to distort under an electric field, often depends on the local chemical environment. For example, the polarizability of a chloride ion is larger in gas phase compared to a chloride ion solvated in water. This effect is due to the restriction the Pauli exclusion principle places on the allowed electron states. Because no two electrons can occupy the same state, when a highly polarizable atom comes in close contact with other atoms or molecules, the space of allowed states can dramatically decrease. This constraint suggests that an accurate molecular mechanics polarizability model should depend on the radial distance between neighboring atoms. This paper introduces a variable polarizability model within the framework of the HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field, by damping the polarizability as a function of the orbital overlap of two atoms. This effectively captures the quantum mechanical exchange polarization effects, without explicit utilization of antisymmetrized wave functions. We show that the variable polarizability model remarkably improves the two-body polarization energies and three-body energies of ion-ion and ion-water systems. Under this model, no manual tuning of atomic polarizabilities for monatomic ions is required; the gas-phase polarizability can be used because an appropriate damping function is able to correct the polarizability at short range.

On closed-shell interactions between heavy main-group elements.

A series of di- and polymetal complexes involving closed-shell, heavy main-group atoms and ions shows a selection of special physical properties. These involve short metal-metal contacts, low entropies of formation and, most interestingly, strong Raman bands at low wavenumbers. These results together with the constitution of the coordination compounds, where the majority of electrons are assembled on the highly polarizable metal atoms and ions, experimental results have been interpreted in terms of direct, partial covalent metal-metal bonding. Previous theoretical studies have challenged this view and instead attributed the obvious attractive forces involved to secondary-type of interactions, such as dispersion. This study utilizes a multitude of theoretical tools, such as natural bond order (NBO) and natural energy decomposition analysis (NEDA), non-covalent interaction (NCI) analysis, electron localization functions (ELFs), and atoms-in-molecules (AIM) to characterize the interactions in models comprising closed-shell dimers, as well as experimentally studied ring and cage systems constituting the main reason for the hypotheses on metal-metal interactions. The results show that all experimental results can be attributed to the covalent interactions between the electron-rich, metal centers and the bridging anions in ring and cage coordination compounds of high symmetry, where the experimentally observed effects can be traced to the combination of covalent interactions between the metal centers and the anions along the edges of the ring and cage systems in combination with the cooperative effects generated by the high symmetry of these ring and cage systems.

C-H⋅⋅⋅X-C bonds in alkyl halides drive reverse selectivities in confined spaces

Binding of non-activated alkyl halides (2–20) in water-soluble cavitand (1) through supramolecular forces is here reported, with emphasis on the role of size and polarizability of the halogen atom in the formation of intramolecular C-H hydrogen bonds in confined spaces. Rare reverse affinity in water (RI < RBr < RCl) is surprisingly observed for the more water-soluble short alkyl halides in dynamic open-ended containers. Competitive bindings and theoretical calculations confirm the unusual selectivity and the presence of C-H hydrogen bonds in non-activated systems for the first time, pointing out the importance and effect of subtle forces on molecular recognition in confined spaces.

Fock-space perturbed relativistic coupled-cluster theory for electric dipole polarizability of one-valence atomic systems: Application to Al and In

We have developed a Fock-space relativistic coupled-cluster theory based method for the calculation of electric dipole polarizability of one-valence atoms and ions. We employ this method to compute the ground-state and spin-orbit coupled excited state electric dipole polarizability of Al and In. To check the quality of many-electron wavefunctions, we also compute the excitation energies of some low-lying states of Al and In. The effects of Breit interaction and QED corrections from the Uehling potential and the self-energy are included to improve the accuracy of $\alpha$ further. Our recommended value of ground-state $\alpha$ for both atoms are in good agreement with the previous theoretical results. From our computations, we find that more than 65\% of contributions come from the dipolar mixing of $3p$($5p$) with $3d$($5d$) and $4s$($6s$)-electrons for Al(In). The largest Breit and QED contributions are found to be 1.3\% and 0.6\%, respectively.

Polarisabilities of iterated stockholder atoms

Polarisabilities of atoms within molecules can be calculated from molecular electron densities using the density partitioning method known as Iterated Stockholder Atoms (ISA). Non-local polarisation effects are removed by optimising the ISA functional for the perturbed electron density, with the additional constraint that the atomic charges do not change. The resulting atomic polarisabilities are chemically reasonable, tend to become smaller as the atomic charge becomes more positive, and are approximately transferable between atoms in similar chemical environments. The methodology can be extended to calculate local higher-rank polarisabilities and dispersion energy coefficients.

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.