Molecular Polarizability Research Articles

Electron interactions with analogous of DNA/RNA nucleobases: 3-hydroxytetrahydroFuran and α-Tetrahydrofurfuryl alcohol

We report quantitative results for electron induced molecular processes for DNA/RNA nucleobase analogous bio-molecules, 3-hydroxytetrahydrofuran (C4H8O2, 3hTHF) and α-tetrahydrofurfuryl alcohol (C5H10O2, THFA), which are similar in structure and functional group to backbone of DNA and RNA. We have employed spherical complex optical potential (SCOP) formalism to compute total elastic (Qel) and inelastic (Qinel) cross sections and used Complex Scattering Potential-ionization contribution (CSP-ic) method to obtain total ionization (Qion) and summed total excitation (∑Qexc) cross sections. These results obtained for a wide energy range (10 eV - 5 keV) may serve as the input parameters in predicting damage in biomolecular systems induced by secondary electrons caused by primary ionization radiation. We have observed a correlation between maximum Qion and molecular polarizability volume (α), ionisation energy (IE) and number of valence electrons (Nv). This work includes an attempt to estimate ∑Qexc for these molecules in normal state.

Novel insights into the predominant factors affecting the bioavailability of polycyclic aromatic hydrocarbons in industrial contaminated areas using PLS-developed model

Bioavailability is recognized as a useful technical standard for risk assessment and pollution rehabilitation. However, knowledge on the bioavailability of polycyclic aromatic hydrocarbons (PAHs) in contaminated site soils is still limited, especially concerning the influential mechanism. With an abundance of soil collections from nine industrial areas in China, the bioavailabilities, as conceptually defined as bioconcentration factors (BCFs) of PAHs were analyzed using biomimetic extraction of hydroxypropyl-β-cyclodextrin (HPCD). Apart from the total content of PAHs varying with the different pyrogenic sources, the BCFs were greatly dependent on the soil physicochemical properties from the spatial scale and inversely proportional to the number of rings. Pearson correlation analysis indicated a weak relationship between bioavailability and the soil dissolved organic matter (DOM), pH and particle size. To incorporate the soil physicochemical properties and structural characteristics of PAHs determined by density functional theory (DFT), the optimum model for bioavailability was developed for BCFs by partial least square (PLS) analysis. The PLS-derived model was shown to be predictive within the applicability domain (AD). The structural characteristics, e.g., molecular polarizability and frontier orbital energy level that favor the soil adsorption of PAH isomers via dispersion interactions, and electron exchanges were indicated to be more impactful on bioavailability than soil environmental factors. However, soil factors should not be neglected, because the pH, DOM, etc. were significantly influential. It makes sense that the higher DOM causes greater bioavailability via increasing the free-dissolved fractions of PAHs. Interestingly, the effect of pH on bioavailability was spectrally validated by excitation-emission matrix (EEM) fluorescence, showing that the interaction between DOM and pyrene strengthened the fluorescence quenching of chromophores with the decline in pH.

Direct pumping of polar fluids with traveling-wave dielectrophoresis.

Efficiently pumping fluids without moving parts in extremely miniaturized formats is challenging. Here, we propose and numerically explore a new type of fluid pump in which a series of electrodes driven at different phases produce a force directly on the molecules of the fluid. This effect is based on traveling-wave dielectrophoresis (twDEP), which has been observed to drive the motion of colloidal particles. Here, we leverage the time needed for fluid molecules with permanent dipoles to align with the applied field to maintain a phase lag between the applied field and the molecular polarization. While requiring operation in the GHz range, this effect is predicted to be efficient due to its ability to directly drive bulk fluid motion. We begin by establishing the foundational equations for this effect and performing finite element simulations to determine its magnitude in a model geometry. By combining theory and a systematic series of calculations, we validate that twDEP pumps should exhibit a fluid flow that scales as the voltage squared divided by the electrode period and that it should increase with the complex permittivity of the fluid and decrease with increasing viscosity. This results in a general equation that predicts the performance of twDEP pumps. Collectively, these computations provide a blueprint for producing twDEP pumps of polar fluids such as water and ethanol. We conclude by noting that the growing interest in high power microwave technology along with metasurfaces to locally tailor phase could provide a path to realizing twDEP pumps in practice.

Data-driven tailoring of molecular dipole polarizability and frontier orbital energies in chemical compound space.

Understanding correlations - or lack thereof - between molecular properties is crucial for enabling fast and accurate molecular design strategies. In this contribution, we explore the relation between two key quantities describing the electronic structure and chemical properties of molecular systems: the energy gap between the frontier orbitals and the dipole polarizability. Based on the recently introduced QM7-X dataset, augmented with accurate molecular polarizability calculations as well as analysis of functional group compositions, we show that polarizability and HOMO-LUMO gap are uncorrelated when considering sufficiently extended subsets of the chemical compound space. The relation between these two properties is further analyzed on specific examples of molecules with similar composition as well as homooligomers. Remarkably, the freedom brought by the lack of correlation between molecular polarizability and HOMO-LUMO gap enables the design of novel materials, as we demonstrate on the example of organic photodetector candidates.

Size dependence of optical nonlinearity for H-capped carbon chains, H-(CC)n-H (n = 3-15): analysis of its nature and prediction for long chains.

Based on a computational approach that can accurately describe their geometric structures and electronic spectra, we have theoretically studied the nonlinear optical (NLO) properties of H-capped carbon chains, H-(CC)n-H (n = 3-15), for the first time. Special attention was paid to the size dependence of the molecular (hyper)polarizability of these species through the nonlinear fitting of the data, which formed two power-law formulas of αiso(∞) = -0.206 + 0.264n1.498 and γ‖(∞) = -0.624 + 0.006n3.368 and was thoroughly discussed at the electronic structure level by in-depth wavefunction analyses. The fundamental gap (ΔE) between vertical ionization energy (VIE) and vertical electron affinity (VEA) is found to be related to the molecular (hyper)polarizability. The calculated (hyper)polarizability of the carbon chains H-(CC)n-H (n = 3-15) is more sensitive to the density functional theory (DFT) applied than to the basis set selected. The results are expected to provide theoretical guidance for the property prediction of arbitrarily long carbon chains not yet synthesized.

Modulation of chiral spectral deflection by van der Waals force-induced molecular electropolarization in catenane oligomers.

The striking chiral optical properties of carbon nanostructures are closely related to the precise three-dimensional spatial arrangement (interaction) of carbon atoms. This work investigated the chiral optical properties of three different structures of all-benzene catenane and trefoil knot regulated by van der Waals (vdW) forces using density functional theory (DFT) calculations and wave function analysis. We systematically illustrate how molecular electrical polarization modulates the chiral optical deflection of alkane oligomers under the induction of van der Waals forces. In this work, the UV-vis spectra, transition density matrices (TDM), and electron-hole density diagrams of three molecules have been studied. Combined with a visualization method to represent the effect of molecular polarization on transition electric/magnetic dipole moments (TEDMs\TMDMs), the results show that vdW interactions can induce chirality deflection in polymers. This mechanism provides a clear direction for designing polymers with specific chirality: by modifying the structure, vdW interactions can be generated in specific regions, and then the chirality of the molecule can be precisely regulated. This will help us to establish a strategy for precisely-oriented design of chiral optical materials, and provide guidance for the application and development of optoelectronic materials in specific fields.

Dielectric characterization studies of hydrogen-bonded polar liquids in nonpolar medium using cavity perturbation technique

The dielectric characteristics of polar substances like propan-1-ol, propionaldehyde, isopropyl amine & its equimolar ternary mixtures in benzene are examined at discrete microwave frequency region using the cavity perturbation technique at 6.218 GHz (J-band), 9.880 GHz (X-band), 16.331 GHz (P-band) and 24.951 GHz (K-Band) at room temperature. The minimum energy geometry optimization is performed at 6-311G+ (d, p), 6-311G++ (d, p) basis set with DFT(B3LYP) method for both pure as well as ternary mixtures of propan-1-ol, propionaldehyde & isopropyl amine liquid systems. The dipole moment(s) of these combinations are evaluated using Higasi's approach and verified with theoretical data. The average relaxation times of the ternary solutions are calculated using the Cole-Cole plots. The mean molecular polarizability values of distinct systems of propan-1-ol, propionaldehyde, isopropyl amine, and their ternary solutions are calculated with Lippincott-δ function model. The findings are described through the molecular association between the components by hydrogen bonding.

Comment on "Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin" by O. Kontkanen, D. Biriukov and Z. Futera, Phys. Chem. Chem. Phys., 2023, 25, 12479.

Polarizability is a fundamental property of all molecular systems describing the deformation of the molecular electronic density in response to an applied electric field. The question of whether polarizability of the active site needs to be included in theories of enzymatic activity remains open. Hybrid quantum mechanical/molecular mechanical calculations are hampered by difficulties faced by many quantum-chemistry algorithms to provide sufficiently accurate estimates of the anisotropic second-rank tensor of molecular polarizability. In this Comment, we provide general theoretical arguments for the values of polarizability of the quantum region or a molecule which have to be reproduced by electronic structure calculations.

Electron transfer bridge inducing polarization of nitrogen molecules for enhanced photocatalytic nitrogen fixation.

Ammonia (NH3) plays a crucial role in the production of fertilizers, medicines, fibers, etc., which are closely relevant to the development of human society. However, the inert and nonpolar properties of NN seriously hinder artificial nitrogen fixation under mild conditions. Herein, we introduce a novel strategy to enhance the photocatalytic efficiency of N2 fixation through the directional polarization of N2 by rare earth metal atoms, which act as a local "electron transfer bridge." This bridge facilitates the transfer of delocalized electrons to the distal N atom and redirects the polarization of adsorbed N2 molecules. Taking cerium doped BiOCl (Ce-BiOCl) as an example, our results reveal that the electrons transfer to the distal N atom through the cerium atom, resulting in absorbed nitrogen molecular polarization. Consequently, the polarized nitrogen molecules exhibit an easier trend for NN cleavage and the subsequent hydrogenation process, and exhibit a greatly enhanced photocatalytic ammonia production rate of 46.7 μmol g-1 h-1 in cerium doped BiOCl, nearly 4 times higher than that of pure BiOCl. The original concept of directional polarization of N2 presented in this work not only deepens our understanding of the N2 molecular activation mechanism but also broadens our horizons for designing highly efficient catalysts for N2 fixation.

Physical Mechanism of Spectra in Carbon Nanobelts under Quantum Size Effect.

Since the successful synthesis of [6,6]carbon nanobelt (CNB), [8,8]CNB and [12,12]CNB have been synthesized successively. CNBs with different sizes ([2N,2N]CNB; N = 2, 3, 4, 5, 6, 7, and 8) have quantum size effects and exhibit completely different optical properties. In this work, the linear and nonlinear optical properties and spectral changes of [2N,2N]CNB are studied based on density functional theory (DFT). The molecular volume, pore volume, and stability of [2N,2N]CNB are investigated. The electron transition mechanism of the one-photon absorption (OPA) and two-photon absorption (TPA) spectra of [2N,2N]CNB is explained, and the extrapolation formula between the wavelength of the absorption peak and the absorption coefficient (ε) and size is given. The infrared (IR) and Raman spectra of [2N,2N]CNB are calculated, and the vibrational modes of characteristic peaks are provided. Finally, the nonlinear optical properties of [2N,2N]CNB are studied, which reflect the anisotropy of molecular polarization. The extrapolation formulas for the polarizability (α) and second hyperpolarizability (γ) of [2N,2N]CNB under different external fields are given. The extrapolation formulas given in this work will help to predict the linear and nonlinear optical properties of arbitrary [2N,2N]CNB beyond computational power, laying the foundation for the practical application of [2N,2N]CNB's theoretical basis.

Quantitative Relationships Between Structure and Activity of Gamma-Carboline Derivative Compounds as Anti-Bovine Viral Diarrhea Virus (BVDV) Using Semi-Empirical AM1 Method

This research aims to study the quantitative structure and activity relationship (QSAR) of gamma-carboline derivative compounds as anti-BVDV agents to get an equation that can predict the value of the anti-BVDV activity of gamma-carboline derived compounds. The research material is experimental EC50 data that convert to anti-BVDB activity. 14 gamma-carboline derivative compounds are divided into 2 groups, namely, 11 fitting compounds and 3 test compounds. QSAR analysis is based on multilinear regression calculations of the fitting compound by plotting the EC50 log as the dependent variable and the descriptor as the independent variable. The used descriptors are atomic net charge (q) and dipole moment (µ), which are involved in calculations using the AM1 semiempirical quantum mechanics method. In addition, the partition coefficient of n-octanol/water (Log P), molecular polarizability (α), molecular weight (BM), Van Der Waals surface area (A vdw), Van Der Waals volume (V vdw), and index of refraction (RD) are obtained from QSAR properties. The resulting QSAR equation is: Log pEC50 = -48.670 – 124.801 (qC11) – 12.661 (α) – 0.918 (µ) – 0.876 (RD) – 0.999 (Log P) + 1.863 (BM) + 0.043 (V vdw) with n = 14; r = 0.937; r2 = 0.878; SD = 0.244; Fcount/Ftable = 1.466; PRESS = 0.749; Sig. = 0.02 This equation can be used as an initial guide for designing the structure of new compounds of the gamma-carboline class by considering some of the most influential descriptors. Consequentially, new compounds can be designed that have a smaller predicted EC50 value than the known compounds derived from gamma-carboline.

On the intensity of light scattered by molecular liquids-Comparison of experiment and quantum chemical calculations.

The intensity of light scattered by liquids has been studied for over a century since the valuable microscopic information about the molecules can be obtained, such as the anisotropy of the molecular polarizability tensor or preferred orientations of neighboring molecules. However, in modern dynamic light scattering experiments, the scattering intensity is usually disregarded, unlike in dielectric spectroscopy, which can be considered as a complementary experimental method, where the dielectric strength is routinely evaluated. The reason lies partly on the fact that the exact form of the equations relating the macroscopically measured light scattering intensity to the microscopic properties of the molecules is debated in the literature. Therefore, as a first step, we compare anisotropy parameters from the literature, calculated from light scattering intensities using different equations, with quantum chemical calculations for over 150 medium-sized molecules. This allows us to identify a consistent form of equations. In a second part, we turn to the depolarized light scattering spectra of 13 van der Waals liquids and some mixtures thereof, recorded with a combination of Tandem-Fabry-Perót and Raman spectroscopies, giving direct access to the reorientational dynamics of the molecules. We discuss how the strength of the structural α-relaxation is connected to the anisotropy parameter, what implication this has for the shape of the α-relaxation, how the components of a mixture-also for the case of ionic liquids-can be identified in this way, and how orientational correlation parameters can be extracted. Additionally, we point out for the example of n-alkanes that for highly flexible molecules, the reorientational motion might not be the decisive source of the depolarized scattered light. We also show that light scattering might serve as a sensitive tool to check the accuracy of a conformer ensemble obtained by quantum chemical calculations.

Low-cost novel X-shaped hole transport materials for efficient perovskite solar cells: Molecular modelling of the core and schiff base effects on photovoltaic and photophysical properties

Eight molecules with D-π-D molecular motifs coded HTM(1-4)a,b were designed as efficient symmetric hole transporting materials for perovskite solar cells. These HTMs are composed of different core moieties, such as spiro [fluorene-9,9′-xanthene]-diol (SFO), spiro [fluorene-9,9′-xanthene]-dimethoxy (SFM), benzo [c][1,2,5]thiadiazole (BTD), and biphenyl (BP) and are gaining lot of attention because of their low-cost, reproducible electrical and optical properties in device performance. Detailed information about the energetic of molecular levels (GSOP/ESOP), first singlet excitation energy (E0-0), equilibrium molecular geometry, charge separation, charge transfer, reorganization energies, polarizability and hyperpolarizability, density of states (DOS), solubility and stability of these molecules was attained by systematically performing molecular modeling calculations using density functional theory (DFT) and time dependent-DFT calculations utilizing hybrid density functional B3LYP using the basis set 6–31g(d,p) level of theory as a successful method for predicting the photophysical and photovoltaic properties of these conjugated systems. The results showed that not only the core moieties, but also Schiff-base linkage extended conjugation, have an effect on the photophysical and photovoltaic properties of the proposed HTMs. It was demonstrated that HTMs incorporating SFO (HTM1a,b), SFM (HTM2a,b), and BP (HTM4a,b) achieved better charge transport, high stability values (ηa = 2.11–2.40 eV), low electron-hole binding energy (Eb = 0.16–0.21 eV) than HTM3a,b with BTD core, which improves hole mobility and decreases recombination, all of which improved device photocurrent, which can be attributed to the extended π-conjugation in SFO, SFM and BP cores. These findings are strikingly similar to those of Spiro-OMeTAD (ηa = 2.45 eV, Eb = 0.16 eV), indicating that these HTMs are promising candidates for efficient and cost-effective PSCs. Interestingly, when the stability of HTM(1-4)a and HTM(1-4)b was compared, it was clear that HTM(1-4)a has lower stability than HTM(1-4)b, which could be attributed to the presence of Schiff base CN bonds in HTM(1-4)b, which reduces the molecules stability when compared to HTM(1-4)b, owing to a strong C–C linkage. Meanwhile, HTM(1-4)a outperforms HTM(1-4)b in terms of electronic performance and hole mobility.

Optical Trapping of a Single Molecule of Length Sub-1 nm in Solution

Optical Trapping of a Single Molecule of Length Sub-1 nm in Solution

An in-silico study to gain a comprehensive understanding of the effects of glucosylation on quercetin properties

In order to gain a molecular understanding of why quercetin characteristics are altered by glucosylation, DFT calculations and MD simulations were utilized. According to DFT findings, glucosylation of quercetin altered its structural stability, molecular polarity, molecular polarizability, and Gibbs free energy of transfer, which gives a molecular explanation for the observed alterations in the aqueous solubility and lipophilicity of derivatives. The outcomes of MD simulations also demonstrated how the various hydroxyl groups of quercetin interact with solvent molecules and how glucosylation can have an impact on that. Additionally, it was shown that glucosylation often increased the number of hydrogen bonds and the nonbonded interaction energies between the molecules of the solvent and the solute. The solubility behavior of glucosylated derivatives in water and alcoholic solvents can be reasonably interpreted molecularly using these results, which could suggest approaches for improving the features of these kinds of bioactive compounds.

Distributed Polarizability Model for Covalently Bonded Fullerene Nanoaggregates: Origins of Polarizability Exaltation.

Polarizability exaltation is typical for (C60)n nanostructures. It relates to the ratio between the mean polarizabilities of (C60)n and C60: the first one is higher than the n-fold mean polarizability of the original fullerene. This phenomenon is used in the design of novel fullerene compounds and the understanding of its properties but still has no chemical rationalization. In the present work, we studied the distributed polarizability of (C60)2 and isomeric (C60)3 nanoaggregates with the density functional theory method. We found that polarizability exaltation increases with the size of the nanostructure and originates from the response of the sp2-hybridized carbon atoms to the external electric field. The highest contributions to the dipole polarizability of (C60)2 and (C60)3 come from the most remote atoms of the marginal fullerene cores. The sp3-hybridized carbon atoms of cyclobutane bridges negligibly contribute to the molecular property. A similar major contribution to the molecular polarizability from the marginal atoms is observed for related carbon nanostructures isomeric to (C60)2 (tubular fullerene and nanopeanut). Additionally, we discuss the analogy between the polarizability exaltation of covalently bonded (C60)n and the increase in the polarizability found in experiments on fullerene nanoclusters/films as compared with the isolated molecules.

The evaluation of the interaction potential of two non-polar molecules in Green function approach

In this research, by assuming that the vacuum electric field fluctuations can convert a molecule (or an atom) into an oscillating electric dipole, the interaction potential of the two atoms or two non-polar molecules is calculated in terms of the molecular polarizabilities and the distance between them. Considering the net electric field at the position of a molecule as a sum of the vacuum electric field and the electric field due to the induced electric dipole of the other molecule, and substituting in the quadratic stark shift formula, the interaction potential of the two molecules is related to the vacuum electric field correlation function. By writing the interaction potential in terms of the imaginary parts of vector potential Green function tensor components (via the fluctuation- dissipation theorem and Kubo’s formula in statistical mechanics) and computing the required Green function components, the interaction potential between the two molecules is evaluated. The small and large distances limits of the general formula investigated and the consistencies with the previous works are shown.‎

SOTIP is a versatile method for microenvironment modeling with spatial omics data

The rapidly developing spatial omics generated datasets with diverse scales and modalities. However, most existing methods focus on modeling dynamics of single cells while ignore microenvironments (MEs). Here we present SOTIP (Spatial Omics mulTIPle-task analysis), a versatile method incorporating MEs and their interrelationships into a unified graph. Based on this graph, spatial heterogeneity quantification, spatial domain identification, differential microenvironment analysis, and other downstream tasks can be performed. We validate each module’s accuracy, robustness, scalability and interpretability on various spatial omics datasets. In two independent mouse cerebral cortex spatial transcriptomics datasets, we reveal a gradient spatial heterogeneity pattern strongly correlated with the cortical depth. In human triple-negative breast cancer spatial proteomics datasets, we identify molecular polarizations and MEs associated with different patient survivals. Overall, by modeling biologically explainable MEs, SOTIP outperforms state-of-art methods and provides some perspectives for spatial omics data exploration and interpretation.

Core–shell structured PVDF-based copolymer fiber design for high energy storage performance

Polymer-based capacitors are very promising for high-power systems due to their high power density and ultrafast charge–discharge speed, yet reaching high dielectric constant and high breakdown strength simultaneously in dielectric polymers required by high-performance capacitors still remains a huge challenge. Herein, poly(vinylidene fluoride-co-trifluoroethylene) (PVDF-TrFE) and poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) were coaxial electrospun in core–shell structured fibers to create locally inhomogeneous microstructures deliberately. Through adjusting the functional group HFP/TrFE monomer ratio, P(VDF-HFP)/P(VDF-TrFE) hybrid polymer films with topological composition distribution have been elaborately designed, enabling gradient polarization distribution from core to shell. Compared with homogeneous hybrid films of the same composition, the core–shell structure significantly boosts breakdown strength, thus resulting in a significantly improved energy storage capacity. At an HFP/TrFE monomer ratio of 10:1, an optimal comprehensive energy storage performance has been achieved with Ue ∼ 20.7 J/cm3 and efficiency 67.8%; moreover, the film could maintain its energy storage performance after 106 charge/discharge cycles without reduction. Molecular dynamic simulation and finite element analysis have been employed in combination to reveal the dipole moments distribution at the molecular level and polarization distribution at the microscale, which further demonstrates that elaborate polarization distribution adjustment is an effective strategy toward high-performance electrostatic energy storage capacitors.

Harnessing Keto‐Enol Tautomerism to Modulate β‐Ketoenamine‐based Covalent Organic Frameworks for Visible‐Light‐Driven CO2 Reduction

AbstractCovalent organic frameworks (COFs) have attracted extensive attention as promising photocatalysts for CO2 reduction. However, there are few reports on the relationship between keto‐enol tautomerism and COFs photocatalyst activity. Three different β‐ketoenamine‐based COFs were prepared by varying the proportion of hydroxyl units in the aldehyde precursor, in which only the HCOF‐2 shows the structural features of the reversible keto‐enol tautomerism. Through density functional theory (DFT) calculations and experiments, the effects of keto‐enol tautomerism on the light absorption intensity, band position, band gap, and carrier separation of these COFs were investigated. The reversible keto‐enol tautomerism contributes to narrowing the band gap and promoting the light absorption capacity. In addition, the reversible keto‐enol tautomerism leads to molecular polarization, which promotes the separation and transmission of carriers within the material. As a result, HCOF‐2 exhibits optimal photocatalytic activity, yielding 309 and 96 μmol g−1 of CO and CH4 respectively within 10 h. This work provides an explanation of the relationship between keto‐enol tautomerism and photocatalytic activity.