Electrostatic Potential Research Articles

Molecular Insights into the Dual Promotion-Inhibition Effects of NaCl at Various Concentrations on the CO2 Hydrate Growth: A Molecular Simulation Study.

Hydrate-based CO2 storage in the ocean is considered a potential method for mitigating the greenhouse effect. Numerous studies demonstrated that NaCl exhibited the dual effects of promotion and inhibition in the nucleation and growth processes of CO2 hydrate, whose mechanisms remain unclear. In this study, the effects of NaCl at various concentrations on the CO2 hydrate growth and crystal are investigated. The independent gradient model based on Hirshfeld partition, electrostatic potential, and binding energy is conducted to study the interaction between ions and water molecules. The motion trajectories of ions are observed at the molecular level to reflect the impact of ion motion on hydrate growth. The results show that the influence of NaCl on hydrate growth depends on a delicate balance of dual promotion-inhibition effects. NaCl can combine more water molecules and provide a transport channel of CO2 to promote hydrate growth at low concentrations. Meanwhile, the promoting effects shift toward inhibition with increasing NaCl concentrations. In a word, this paper proposes a novel mechanism for the dual promotion-inhibition effects of NaCl on hydrate growth, which is significant for further research on hydrate-based CO2 storage in the ocean.

AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening.

Ligand-based virtual screening (LBVS) can be pivotal for identifying potential drug leads, especially when the target protein's structure is unknown. However, current LBVS methods are limited in their ability to consider the ligand conformational flexibility. This study presents AutoDock-SS (Similarity Searching), which adapts protein-ligand docking for use in LBVS. AutoDock-SS integrates novel ligand-based grid maps and AutoDock-GPU into a novel three-dimensional LBVS workflow. Unlike other approaches based on pregenerated conformer libraries, AutoDock-SS's built-in conformational search optimizes conformations dynamically based on the reference ligand, thus providing a more accurate representation of relevant ligand conformations. AutoDock-SS supports two modes: single and multiple ligand queries, allowing for the seamless consideration of multiple reference ligands. When tested on the Directory of Useful Decoys─Enhanced (DUD-E) data set, AutoDock-SS surpassed alternative 3D LBVS methods, achieving a mean AUROC of 0.775 and an EF1% of 25.72 in single-reference mode. The multireference mode, evaluated on the augmented DUD-E+ data set, demonstrated superior accuracy with a mean AUROC of 0.843 and an EF1% of 34.59. This enhanced performance underscores AutoDock-SS's ability to treat compounds as conformationally flexible while considering the ligand's shape, pharmacophore, and electrostatic potential, expanding the potential of LBVS methods.

Atomic Force Microscopy Simulations for CO-functionalized tips with Deep Learning

Abstract Atomic Force Microscopy (AFM) operating in the frequency modulation mode with a metal tip functionalized with a CO molecule \ph{is able to image} the internal structure of molecules with an unprecedented resolution. The interpretation of these images is often difficult, making the support of theoretical simulations important. Current simulation methods, particularly the most accurate ones, require expertise and resources to perform ab initio calculations for the necessary inputs (i.e charge density and electrostatic potential of the molecule). Here, we propose a computationally inexpensive and fast alternative to the physical simulation of these Atomic Force Microscopy (AFM) images based on a Conditional Generative Adversarial Network (CGAN), that avoids all force calculations, and uses as the only input a 2D ball–and–stick depiction of the molecule. We discuss the performance of the model when trained with differ- ent subsets extracted from the previously published QUAM-AFM database. Our CGAN reproduces accurately the intramolecular contrast observed in the simulated images for quasi–planar molecules, but has limitations for molecules with a substantial internal corrugation, due to the strictly 2D character of the input.

An in-depth investigation of nonlinear optical properties of self-assembled borophene doped with P7Ba2NO3: a computational simulating study

Density functional theory was used to conduct a theoretical analysis of super salt doped on borophene. With the LanL2DZ basis set, which is appropriate for metal atoms, the B3LYP technique was used. Numerous analyses were used to characterize the structural properties, such as molecular geometry, frontier molecular orbital, non-covalent interaction, electron density difference map, molecular electrostatic potential, Density of States (DOS), UV–vis spectroscopy and infrared vibrational spectra analysis. The nonlinear optical characteristics were investigated through polarizability as well as hyperpolarizability calculations theoretically. The values were noticeably greater than those of borophene in all the above results. Compared to borophene, which has a hardness value of 0.905 eV, all the complexes exhibited small values of hardness, ranging from 0.41 eV to 0.795 eV. In addition, it was found that all the complexes had lower excitation energies as opposed to the greater excitation energy of borophene. Due to its lowest excitation energy (E), Boro@SS4 showed a striking increase in average polarizability ( αo = 847.13 au) in addition average first hyperpolarizability ( β0 = 540007.60 au) in comparison to borophene ( αo = 593.75 au and β0 = 383.76 au).

Coupled exciton internal and center-of-mass motions in two-dimensional semiconductors by a periodic electrostatic potential

Coupled exciton internal and center-of-mass motions in two-dimensional semiconductors by a periodic electrostatic potential

Mutation of Disulfide Bond Sites Reduces the Immunoreactivity of Cra a 4 by Changing the Structural Characteristics.

Sarcoplasmic calcium-binding protein (Cra a 4) from Crassostrea angulata belongs to the EF-hand superfamily, and understanding of its structure-allergenicity relationship is still insufficient. In this study, chemical denaturants were used to destroy the structure of Cra a 4, showing that disruption of the structure reduced its IgG-/IgE-binding activity. To explore which critical amino acid site affects the allergenicity of Cra a 4, the mutants were obtained by site-directed mutations in the disulfide bonds site (C97), conformational epitopes (I105, D114), or Ca2+-binding region (D106, D110) and their IgG-/IgE-binding activity was reduced significantly using serological tests. Notably, C97A had the lowest immunoreactivity. In addition, two conformational epitopes of Cra 4 were verified. Meanwhile, the increase of the α-helical content, surface hydrophobicity, and surface electrostatic potential of C97A affected its allergenicity. Overall, the understanding of the structure-allergenicity relationship of Cra a 4 allowed the development of a hypoallergenic mutant.

Constructing Directional Electrostatic Potential Difference via Gradient Nitrogen Doping for Efficient Oxygen Reduction Reaction.

Nitrogen doping has been recognized as an important strategy to enhance the oxygen reduction reaction (ORR) activity of carbon-encapsulated transition metal catalysts (TM@C). However, previous reports on nitrogen doping have tended to result in a random distribution of nitrogen atoms, which leads to disordered electrostatic potential differences on the surface of carbon layers, limiting further control over the materials' electronic structure. Herein, a gradient nitrogen doping strategy to prepare nitrogen-deficient graphene and nitrogen-rich carbon nanotubes encapsulated cobalt nanoparticles catalysts (Co@CNTs@NG) is proposed. The unique gradient nitrogen doping leads to a gradual increase in the electrostatic potential of the carbon layer from the nitrogen-rich region to the nitrogen-deficient region, facilitating the directed electron transfer within these layers and ultimately optimizing the charge distribution of the material. Therefore, this strategy effectively regulates the density of state and work function of the material, further optimizing the adsorption of oxygen-containing intermediates and enhancing ORR activity. Theoretical and experimental results show that under controlled gradient nitrogen doping, Co@CNTs@NG exhibits significantly ORR performance (Eonset=0.96V, E1/2=0.86V). At the same time, Co@CNTs@NG also displays excellent performance as a cathode material for Zn-air batteries, with peak power density of 132.65mAcm-2 and open-circuit voltage (OCV) of 1.51V. This work provides an effective gradient nitrogen doping strategy to optimize the ORR performance.

Nonlinear oscillations of dust‐acoustic waves in non‐Maxwellian dusty plasma under the gravitational force effect

AbstractIn this paper, the role of dust grain's gravitational force on the nonlinear dust‐acoustic oscillations in non‐Maxwellian dusty plasma is analyzed. It is shown that increasing the number of non‐thermal ions causes the diminution of the electrostatic potential's amplitude and a reduction in the number of oscillations introduced by the gravitational force. We have also found that reducing the size of the dust grain induces qualitatively the same effects as an increase in the number of non‐thermal ions and when the gravitational force is considered, the electric charge exhibits oscillatory profile and becomes less negative far away from the origin. This result may be interesting in the study of astrophysical plasmas where the electromagnetic force is smaller than the gravitational one such as in the Halley Comet.

Engineering Professors' Conceptions on the Conceptual Field of Electrostatics in Mexico

This study explores the conceptual understanding of electromagnetism among physics professors at the Aeronautical University in Querétaro, Mexico. While student misconceptions in electromagnetism have been extensively studied, research on professors' understanding and its potential impact remains limited (Pardhan & Bano, 2001). This research aims to address this gap by focusing on the core concepts of electrostatic force, electric field, and electric potential. Eight professors participated in the study. Their academic background, electromagnetism course history, and teaching experience were documented. A three-tier diagnostic test, based on Vergnaud's theory of conceptual fields, was then used to assess their conceptualisation of these concepts and their interrelationships. The analysis revealed that only one professor consistently demonstrated correct understanding across all three concepts. Interestingly, this professor was also the one with the most extensive teaching experience in the subject. The results suggest a potential connection between teaching experience and a deeper conceptual understanding of electromagnetism. Further research is needed to explore this connection and its implications for mitigating student misconceptions through effective teaching practices.

Zn(II), Mn(III), and Co(III) complexes of Schiff base derived from 2‐hydroxy‐1‐naphthaldehyde: Synthesis, spectral surveys, single crystal structure studies, Hirshfeld surface analysis, density functional theory calculation, molecular electrostatic potential, and molecular docking evaluations

A new series of transition metal complexes of bidentate Schiff base compound derived from 2‐hydroxy‐1‐(2‐methoxyethylimino)‐naphthalene (HL) were synthesized and characterized using elemental analysis, Fourier transform infrared spectroscopy (FT‐IR), and UV–vis spectroscopies. X‐ray single crystal structures of Zn(II), Mn(III), and Co(III) complexes (1–4) have also been determined, and it was indicated that these Zn(II) and Co(III) complexes (1, 4) are in an octahedral geometry. Whereas, it was found that the Zn complex (2) is in quite a regular tetrahedral environment. Also, the Mn center in complex (3) is ligated by two azomethine nitrogen atoms, two ligand oxygen atoms, and one Cl atom of metal salt forming five coordinated tetragonal pyramid geometry around the Mn atoms. The cyclic voltammetry of the complexes specifies an irreversible redox behavior for all complexes (1–4). Next, DFT/B3LYP theoretical method was used to determine the optimal geometrical configurations and comparison between experimental and theoretical data, as well as for calculations of molecular electrostatic potential, highest‐occupied molecular orbital (HOMO)‐lowest‐unoccupied molecular orbital (LUMO) energy values of selected compounds. The study of non‐covalent interactions was done by Hirshfeld surface analysis using CrystalExplorer program. Furthermore, molecular docking inspection was carried out to study the binding affinity of the tested complexes towards protein B‐cell lymphorna (PDB ID: 4LXD). Using the results obtained from the molecular docking and the summarized interaction of the binding processes, these structures show the validity of effective inhibition against liver cancer.

DFT/TDDFT calculations of geometry optimization, electronic structure and spectral properties of clevudine and telbivudine for treatment of chronic hepatitis B

Chronic hepatitis B remains a worldwide health concern. Presently, many drugs, such as Clevudine and Telbivudine, are recommended for the treatment of chronic hepatitis B disease. For this purpose, the quantum chemical analysis of ELUMO-HOMO (Egap), ionization potential (IP), electron affinity (EA), electronegativity (EN), chemical hardness (η), chemical potential (μ), chemical softness (S), electrophilicity index (ω), electron accepting capability (ω+), electron-donating capability (ω-), Nucleophilicity index (N), additional electronic charge (∆Nmax), Optical softness (σ0) and Dipole Moment, IR and UV–Vis spectra, molecular electrostatic potential (MEP) profile, Mulliken charge analysis, natural bond orbital (NBO) were examined in this study. The dipole moment of the compounds suggests their binding pose and predicted binding affinity. The electrophilic and nucleophilic regions were identified, and techniques such as NBO, UV–Vis, and IR were used to gain insights into the molecular structure, electronic transitions, and potential drug design for Hepatitis B treatment. Calculations for this study were carried out using the Gaussian 09 program package coupled with the DFT/TDDFT technique. The hybrid B3LYP functional method and the 6-311++G(d, p) basis set were used for the calculations.

Synthesis of bis-(benzhydryloxy) substituted axially silicon(IV) phthalocyanine: investigation of photophysical, photochemical, and computational electronic properties

Synthesis of axially disubstituted silicon(IV) phthalocyanine bearing benzhydryloxy groups obtained by reaction of SiPcCl2 with diphenylmethanol is reported. Characterization of the compound was performed by 1H and 13C NMR, UV–Vis, mass spectrometry, and FT-IR spectroscopy. Photophysical and photochemical properties were investigated. Fluorescence spectra measurements were performed in DMSO as solvent. A preferred chemical method was used to determine the amount of singlet oxygen production. Optimizations were calculated for the single-molecule Si-Pc with the 6–311 G (d, p) basis set at the B3LYP and B3PW91 levels of density functional theory (DFT). The charge transfer (or) charge delocalization between intramolecular donor–acceptor groups was determined by NBO analysis. Furthermore, molecular electrostatic potential, Fukui functions, electrophilic and nucleophilic character maps were calculated. The electronic structure and energy parameters of the investigated compound were determined to be ΔE calc = 2.19 eV by DFT calculation and ΔE opt = 1.84 by experimental UV spectrum.

Potential prediction in aqueous organic redox-targeting flow batteries: DFT calculation and experimental validation

Aqueous organic redox flow batteries (AORFBs) face challenges of low energy density, which can be addressed by the strategy of redox-targeting (RT) reaction integrating solid materials (SMs) with redox mediators (RMs). However, the potential matching between SM and RM is demanding and complex. In this work, we establish a precise density functional theory (DFT) protocol to predict redox potential in RT-AORFB with anthraquinone-2,7-disulfonic acid (AQDS) derivatives as RM and poly(N-anthraquinoyl pyrrole) (PAQPy) as SM. Theoretical redox potentials are calculated from the Gibbs free energy (GFE) of various molecular models. The results suggest a precise potential match for 1,8-dihydroxyanthraquinone-2,7-disulfonic acid (1,8-DHAQDS) and PAQPy (-1.08 V and -1.09 V vs. SHE). Additionally, hydrogen bonding is involved to make simulation results more realistic, demonstrating a positive potential shift with increased GFE difference for both AQDS derivatives and PAQPy. To further elucidate the influencing mechanism of hydrogen bonding, electrostatic potential (ESP) and HOMO-LUMO gap are integrated together with GFE. The results indicate the introduction of hydrogen bonding results in extended distance for electron tunneling and a larger HOMO-LUMO gap, leading to higher GFE difference and a positive potential shift. Remarkably, results of experimental validations agree well with theoretical potential calculation. Based on predictions results, the RT-AORFB is successfully constructed with the well-matched 1,8-DHAQDS and PAQPy, exhibiting a 3.86-fold capacity enhancement compared to blank AORFB with 1,8-DHAQDS. The integrated DFT approach with GFE, ESP and HOMO-LUMO gap in this work emerges as a promising method for accurately predicting redox potentials in RT systems.

Guest Acceptors with Lower Electrostatic Potential in Ternary Organic Solar Cells for Minimizing Voltage Losses.

The ternary strategy, in which one guest component is introduced into one host binary system, is considered to be one of the most effective ways to realize high-efficiency organic solar cells (OSCs). To date, there is no efficient method to predict the effectiveness of guest components in ternary OSCs. Herein, three guest compositions (i.e., ANF-1, ANF-2 and ANF-3) with different electrostatic potential (ESP) are designed and synthesized by modulating the electron-withdrawing ability of the terminal groups through density functional theory simulations. The effects of the introduction of guest component into the host system (D18:N3) on the photovoltaic properties were investigated. The theoretical and experimental studies provide a key rule for guest acceptor in ternary OSCs to improve the open-circuit voltage, that is, the larger ESP difference between the guest and host acceptor, the stronger the intermolecular interactions and the higher the miscibility, which improves the luminescent efficiency of the blend film and the electroluminescence quantum yield (EQEEL) of the device by reducing the aggregation-caused-quenching, thereby effectively decreasing the non-radiative voltage loss of ternary OSCs. This work will greatly contribute to the development of highly efficient guest components, thereby promoting the rapid breakthrough of the 20% efficiency bottleneck for single-junction OSCs. This article is protected by copyright. All rights reserved.

Assessment of uniform charge assumption by investigating electrostatic charge distribution and potential during container filling: A numerical study

Using simulations, this study aims to investigate the actual charge distribution and resulting electrostatic potential during the filling process of a grounded metal barrel with low-conductivity diesel fuel. The flow rates used for loading were proposed based on the assumption of uniform charge distribution. Deviating from the uniform charge assumption, we observed local charge concentrations, including on the surface of the liquid. Despite the excessive surface charge, the maximum surface potential closely aligns with the prediction of the uniform charge assumption. This supports the practical viability of the proposed flow rates. Yet, considering a higher safety factor is advisable.

DFT studies on structure, electronics, bonding nature, NBO analysis, thermodynamic properties, molecular docking, and MM-GBSA evaluation of 4-methyl-3-[2-(4-nitrophenyl)-1,3-dioxo-2,3-dihydro-1H-isoindole-5-amido]benzoic acid: a potent inhibitor of Graves’ disease

AbstractA calculation analysis on the molecular structure and energy of 4-methyl-3-[2-(4-nitrophenyl)-1,3-dioxo-2,3-dihydro-1H-isoindole-5-amido]benzoic acid (COD30) is carried out with the 6-311G (d,p) basis set by the DFT/RB3LYP method as an anti-graves' disease treatment. The calculated FT-IR spectrum is strongly correlated with the vibrational spectra reported in the literature. To evaluate the entire electron density and organic reactive sites of COD30, molecular electrostatic potential (MEP) and frontier molecular orbitals (FMO) were analyzed. The density of states analysis is used to determine the orbital molecular contributions (DOS and PDOS). In comparison to methimazole (MMI) and propylthiouracil, COD30 showed more encouraging docking results, and it also offered golden binding contacts in addition to an improvement in docking energy (PTU). The outcomes of bioactivity prediction and MD simulation indicate that COD30 could be further developed into an inhibitor of Graves' disease.

DFT and TDDFT exploration on electronic transitions and bonding aspect of DPA and PTDC ligated transition metal complexes.

In this study, we have investigated the structure, reactivity, bonding, and electronic transitions ofDPAandPDTC along with theirNi-Zncomplexes usingDFT/TD-DFT methods. The energy gap between the frontier orbitals was computed to understand the reactivity pattern of the ligands and metal complexes. From the energies of FMO's, the global reactivity descriptors such as electron affinity, ionization potential, hardness (η), softness (S), chemical potential (μ), electronegativity (χ), and electrophilicity index (ω) have been calculated. The complexes show a strong NLO properties due to easily polarization as indicated by the narrow HOMO-LUMO gap. The polarizability and hyperpolarizabilities of the complexes indicate that they are good candidates for NLO materials. Molecular electrostatic potential (MEP) maps identified electrophilic and nucleophilic sites on the surfaces of the complexes. TDDFT and NBO analyses provided insights into electronic transitions, bonding, and stabilizing interactions within the studied complexes. DPA and PDTC exhibited largerHOMO-LUMO gapsand more negative electrostatic potentials compared to their metal complexes suggesting the higher reactivity. Ligands (DPA and PDTC) had absorption spectra in the range of250nm to 285nm while their complexes spanned250nm to 870nm. These bands offer valuable information on electronic transitions, charge transfer and optical behavior. This work enhances our understanding of the electronic structure and optical properties of these complexes. Gaussian16 program was used for the optimization of all the compounds. B3LYP functional in combination with basis sets, such as LanL2DZ for Zn, Ni and Cu while 6-311G** for other atoms like C, H, O, N, and S was used. Natural bond orbital (NBO) analysis is carried out to find out how the filled orbital of one sub-system interacts with the empty orbital of another sub-system. The ORCA software is used for computing spectral features along with the zeroth order regular approximation method (ZORA) to observe its relativistic effects. TD-DFT study is carried out to calculate the excitation energy by using B3LYP functional.

Regulating Surface-Passivator Binding Priority for Efficient Perovskite Light-Emitting Diodes.

Suppressing trap-assisted nonradiative losses through passivators is a prerequisite for efficient perovskite light-emitting diodes (PeLEDs). However, the complex bonding between passivators and perovskites severely suppresses the passivation process, which still lacks comprehensive understanding. Herein, the number, category, and degree of bonds between different functional groups and the perovskite are quantitatively assessed to study the passivation dynamics. Functional groups with high electrostatic potential and large steric hindrance prioritize strong bonding with organic cations and halides on the perfect surface, leading to suppressed coordination with bulky defects. By modulating the binding priorities and coordination capacity, hindrance from the intense interaction with perfect perovskite is significantly reduced, leading to a more direct passivation process. Consequently, the near-infrared PeLED without external light out-coupling demonstrates a record external quantum efficiency of 24.3% at a current density of 42mA cm-2. In addition, the device exhibits a record-level-cycle ON/OFF switching of 20000 and ultralong half-lifetime of 1126.3h under 5mA cm-2. A deep understanding of the passivators would offer new insights into the development of high-performance PeLEDs. This article is protected by copyright. All rights reserved.

Proposed Quantum Twisting Scanning Probe Microscope over Twisted Bilayer Graphene.

Twisted bilayer graphene (TBG) has the natural merits of tunable flat bands and localized states distributed as a triangular lattice. However, the application of this state remains obscure. By density functional theory (DFT) and pz orbital tight-binding model calculations, we investigate the tip-shaped electrostatic potential of top valence electrons of TBG at half filling. Adsorption energy scanning of molecules above the TBG reveals that this tip efficiently attracts molecules selectively to AA-stacked or AB-stacked regions. Tip shapes can be controlled by their underlying electronic structure, with electrons of low bandwidth exhibiting a more localized feature. Our results indicate that TBG tips offer applications in noninvasive and nonpolluting measurements in scanning probe microscopy and theoretical guidance for 2D material-based probes.

Particle simulation of the confinement of the plasma blanket in the magnetic mirror

A new guiding center particle code Guiding center Mirror Simulation is developed to simulate the evolution and confinement of the axisymmetric plasma blanket in the magnetic mirror field generated by a pair of Helmholtz coils. The simulation results indicate that this plasma blanket maintains its shape throughout evolution, and the steady state distributions of both density and electrostatic potential are obtained. The correlation between the plasma density and the characteristic confinement time is also investigated. Generally, the characteristic confinement time decreases with increasing density. When the density is low enough, it is approximately the pitch angle scattering time of the trapped electrons. When the density increases, it comes to several times of the ion transit time evaluated with the Bohm velocity. These results have the potential for experimental applications.