Electron Density Research Articles

DFT, Molecular Docking, Bioactivity and ADME Analyses of Vic-dioxim Ligand Containing Hydrazone Group and its Zn(II) Complex.

Cancer is one of the diseases affecting a large population worldwide and resulting in death. Finding new anti-cancer drugs that are target-focused and have low toxicity is of great importance. This study aimed to investigate the effects of vic-dioxime derivatives carrying hydrazone group and its Zn(II) complex on cancer using molecular docking, bioactivity and quantum chemical calculations. Molecular docking studies were performed on epidermal growth factor receptor and vascular endothelial growth factor receptor 2 target proteins. Furthermore, molecular geometry was performed, and the frontier molecular orbitals, Mulliken charges and molecular electron density distribution were evaluated using density functional theory. Also, the bioactivity parameters of the compounds were evaluated, and ADME analysis was performed using web-based tools. Higher binding affinity was observed for Zn(II) complex with target proteins vascular endothelial growth factor receptor 2 and against epidermal growth factor receptor when compared with LH2. Only the Zn(II) complex against the epidermal growth factor receptor had ligand efficiency and fit quality in the valid range. Furthermore, LH2 has the most potent electrophilic ability (acceptor) among other compounds. Moreover, both LH2 and Zn(II) complexes strongly satisfy Lipinski's rule of five. In conclusion, these novel compounds, especially Zn(II) complex, can be new candidates for anticancer drug development studies which are target-focused and have low toxicity.

Development of a single-domain antibody to target a G-quadruplex located on the hepatitis B virus covalently closed circular DNA genome.

To achieve a virological cure for hepatitis B virus (HBV), innovative strategies are required to target the covalently closed circular DNA (cccDNA) genome. Guanine-quadruplexes (G4s) are a secondary structure that can be adopted by DNAand play a significant role in regulating viral replication, transcription, and translation. Antibody-based probes and small molecules have been developed to study the role of G4s in the context of the human genome, but none have been specifically made to target G4s in viral infection. Herein,we describe the development of a humanized single-domain antibody (S10) that can target a G4 located in the PreCore (PreC) promoter of the HBV cccDNA genome. MicroScale Thermophoresis demonstrated that S10 has a strong nanomolar affinity to the PreC G4 in its quadruplex form and a structural electron density envelope of the complex was determined using Small-Angle X-ray Scattering. Lentiviral transduction of S10 into HepG2-NTCP cells shows nuclear localization, and chromatin immunoprecipitation coupled with next-generation sequencing demonstrated that S10 can bind to the HBV PreC G4 present on the cccDNA. This research validates the existence of a G4 in HBV cccDNA and demonstrates that this DNA secondary structure can be targeted with high structural and sequence specificity using S10.

A new model for plasmapause locations derived from IMAGE RPI and Van Allen probe data

The outer boundary of the plasmasphere, the plasmapause, is characterized by a sharp electron density gradient that changes under varying space weather conditions. We developed a new model, called Neustrelitz/ESOC PlasmaPause Model (NEPPM), for providing plasmapause location in terms of -shell utilizing electron density measurements from the Van Allen probes from 2012 to 2018 and the IMAGE satellite data from 2001 to 2005. Both datasets were preprocessed, and algorithms were developed for automatic detection of plasmapause location. The suggested model provides a simple ellipse-based approach determined by the semi-major axis, the eccentricity, and the orientation angle of the semi-major axis. The modelled varies as a function of the index and magnetic local time . The NEPPM results are compared with the Global Core Plasma Model (GCPM). The plasmapause bulge in the evening hours follows the level of geomagnetic activity. The NEPPM will complete the NPSM (Neustrelitz PlasmaSphere Model), which was derived from dual-frequency GPS measurements on-board the CHAMP satellite mission.

Charge Redistribution in Mechanochemical Reactions for Solid Interfaces.

Mechanochemical strategies are widely used in various fields, ranging from friction and wear to mechanosynthesis, yet how the mechanical stress activates the chemical reactions at the electronic level is still open. We used first-principles density functional theory to study the rule of the stress-modified electronic states in transmitting mechanical energy to trigger chemical responses for different mechanochemical systems. The electron density redistribution among initial, transition, and final configurations is defined to correlate the energy evolution during reactions. We found that stress-induced changes in electron density redistribution are linearly related to activation energy and reaction energy, indicating the transition from mechanical work to chemical reactivity. The correlation coefficient is defined as the term "interface reactivity coefficient" to evaluate the susceptibility of chemical reactivity to mechanical action for material interfaces. The study may shed light on the electronic mechanism of the mechanochemical reactions behind the fundamental model as well as the mechanochemical phenomena.

Customized modulation on plasma uniformity by non-uniform magnetic field in capacitively coupled plasma

A two-dimensional fluid model based on COMSOL Multiphysics is developed to investigate the modulation of static magnetic field on plasma homogeneity in a capacitively coupled plasma (CCP) chamber. To generate a static magnetic field, direct current is applied to a circular coil located at the top of the chamber. By adjusting the magnetic field’s configuration, which is done by altering the coil current and position, both the plasma uniformity and density can be significantly modulated. In the absence of the magnetic field, the plasma density exhibits an inhomogeneous distribution characterized by higher values at the plasma edge and lower values at the center. The introduction of a magnetic field generated by coils results in a significant increase in electron density near the coils. Furthermore, an increase in the sets of coils improves the uniformity of the plasma. By flexibly adjusting the positions of the coils and the applied current, a substantial enhancement in overall uniformity can be achieved. These findings demonstrate the feasibility of using this method for achieving uniform plasma densities in industrial applications.

Emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations.

We present in this work the emle-engine package (https://github.com/chemle/emle-engine)─the implementation of a new machine learning embedding scheme for hybrid machine learning potential/molecular-mechanics (ML/MM) dynamics simulations. The package is based on an embedding scheme that uses a physics-based model of the electronic density and induction with a handful of tunable parameters derived from in vacuo properties of the subsystem to be embedded. This scheme is completely independent of the in vacuo potential and requires only the positions of the atoms of the machine learning subsystem and the positions and partial charges of the molecular mechanics environment. These characteristics allow emle-engine to be employed in existing QM/MM software. We demonstrate that the implemented electrostatic machine learning embedding scheme (named EMLE) is stable in enhanced sampling molecular dynamics simulations. Through the calculation of free energy surfaces of alanine dipeptide in water with two different ML options for the in vacuo potential and three embedding models, we test the performance of EMLE. When compared to the reference DFT/MM surface, the EMLE embedding is clearly superior to the MM one based on fixed partial charges. The configurational dependence of the electronic density and the inclusion of the induction energy introduced by the EMLE model leads to a systematic reduction in the average error of the free energy surface when compared to MM embedding. By enabling the usage of EMLE embedding in practical ML/MM simulations, emle-engine will make it possible to accurately model systems and processes that feature significant variations in the charge distribution of the ML subsystem and/or the interacting environment.

Quality assurance of an established online adaptive radiotherapy program: patch and software upgrade

IntroductionThe ability to dynamically adjust target contours, derived Boolean structures, and ultimately, the optimized fluence is the end goal of online adaptive radiotherapy (ART). The purpose of this work is to describe the necessary tests to perform after a software patch installation and/or upgrade for an established online ART program.MethodsA patch upgrade on a low-field MR Linac system was evaluated for post-software upgrade quality assurance (QA) with current infrastructure of ART workflow on (1) the treatment planning system (TPS) during the initial planning stage and (2) the treatment delivery system (TDS), which is a TPS integrated into the delivery console for online ART planning. Online ART QA procedures recommended for post-software upgrade include: (1) user interface (UI) configuration; (2) TPS beam model consistency; (3) segmentation consistency; (4) dose calculation consistency; (5) optimizer robustness consistency; (6) CT density table consistency; and (7) end-to-end absolute ART dose and predicted dose measured including interruption testing. Differences of calculated doses were evaluated through DVH and/or 3D gamma comparisons. The measured dose was assessed using an MR-compatible A26 ionization chamber in a motion phantom. Segmentation differences were assessed through absolute volume and visual inspection.Results(1) No UI configuration discrepancies were observed. (2) Dose differences on TPS pre-/post-software upgrade were within 1% for DVH metrics. (3) Differences in segmentation when observed were small in general, with the largest change noted for small-volume regions of interest (ROIs) due to partial volume impact. (4) Agreement between TPS and TDS calculated doses was 99.9% using a 2%/2-mm gamma criteria. (5) Comparison between TPS and online ART plans for a given patient plan showed agreement within 2% for targets and 0.6 cc for organs at risk. (6) Relative electron densities demonstrated comparable agreement between TPS and TDS. (7) ART absolute and predicted measured end-to-end doses were within 1% of calculated TDS.DiscussionAn online ART QA program for post-software upgrade has been developed and implemented on an MR Linac system. Testing mechanics and their respective baselines may vary across institutions, but all necessary components for a post-software upgrade QA have been outlined and detailed. These outlined tests were demonstrated feasible for a low-field MR Linac system; however, the scope of this work may be applied and adapted more broadly to other online ART platforms.

Boron-Nitrogen-Edged Biomass-Derived Carbon: A Multifunctional Approach for Colorimetric Detection of H2O2, Flame Retardancy, and Triboelectric Nanogenerator.

Enhancing the concentration and type of nitrogen (N) dopants within the Sp2-carbon domain of carbon recycled from biomass sources is an efficient approach to mimic CNT, GO, and rGO to activate oxidants such as H2O2, excluding toxic chemicals and limiting reaction steps. However, monitoring the kind and concentration of N species in the Sp2-C domain is unlikely with thermal treatments only. A high temperature for graphitization reduces N moieties, leading to low electron density. This inhibits H2O2 adsorption and activation on catalyst surfaces. In this study, coffee waste (CW) is converted into B, N-doped biochar (BXNbY) using boric acid-assisted pyrolysis (H3BO3mass = X and carbonization temperature = Y) under N2 to overcome the challenge. The B dopant regulates the concentration and type of N, provides Lewis's acid sites, and converts graphitic-N to pyridine-N in BXNbY. The optimized B3Nb900 exhibits excellent colorimetric sensing performance toward H2O2 with a low detection limit (36.9nM) and high selectivity in the presence of many interferences and milk samples due to high pyridinic-N and Sp2 domain sizes. Interestingly, B enhances other properties of N-containing CW-derived carbon and introduces self-extinguishing and tribopositive properties. Hence, BXNbY-coated polyurethane foam shows excellent flame retardancy and energy harvesting performance.

Transferability of Buckingham Parameters for Short-Range Repulsion between Topological Atoms.

The repulsive part of the Buckingham potential, with parameters A and B, can be used to model deformation energies and steric energies. Both are calculated using the interacting quantum atom energy decomposition scheme where the latter is obtained from the former by a charge-transfer-based energy correction. These energies relate to short-range interactions, specifically the deformation of electron density and steric hindrance, respectively, when topological atoms approach each other. In this work, we calculate and fit the energies of carbonyl carbon, carbonyl oxygen, and, where possible, amine nitrogen atoms to the repulsive part of the Buckingham potential for 26 molecules. We find that while the steric energies of all atom pairs studied display exponential behavior with respect to distance, some deformation energy data do not. The obtained parameters are shown to be transferable by calculating root-mean-square errors of fitted potentials with respect to energy data of the same atom in, as far as possible, all other molecules from our data set. We observed that 36% and 10% of these errors were smaller than 4 kJ mol-1 for steric and deformation energy, respectively. Thus, we find that steric energy parameters are more transferable than deformation energy parameters. Finally, we speculate about the physical meaning of the A and B parameters and the implications of the strong exponential and exponential-linear piecewise relationships that we observe between them.

Magnetic Component of Quasi-coherent Mode of Plasma Fluctuations in Ohmic Plasma of the T-10 Tokamak

In this work the phenomenon of the quasi-coherent mode of plasma fluctuations in purely ohmic plasmas of the T-10 tokamak is investigated. The plasma magnetic fluctuation spectra along with spectra of relative electron density oscillations and plasma potential fluctuation spectra were studied. The presence of both electrostatic and magnetic components of the quasi-coherent mode has been established in the core and as well at the edge regions of the plasma column. This fact allows one to consider the quasi-coherent mode as one of the types of electromagnetic turbulence of fusion plasma.

Are There Atoms Inside Atomic Anions? H- and Li- Revisited.

Yes, atoms are still there. We show that the inner electrons of H- and Li- behave almost as if the outer electrons were not present and that the effect of electron correlation is such that the outer loosely bound electron tries to stay as close as possible to the nucleus but without interfering too much with the electronic distribution of the inner electrons in such a way that the electronic densities of H and Li are still recognizable inside the respective negative ions. We introduce the concept of partial electronic distribution, one for each electron: a particular decomposition of the electronic density. Equipped with this tool, we analyze the internal structure of the anions to recover the chemical intuition of an atomic negative ion on firm quantum mechanical grounds: that of an atom, almost unperturbed, with a loosely bound electron.

Binding energies and hydrogen bonds effects on DNA-cisplatin interactions: a DFT-xTB study.

A systematic study of hydrogen bonds in base pairs and the interaction of cisplatin with DNA fragments was carried out. Structure, binding energies, and electron density were analyzed. xTB has proven to be an accurate method for obtaining structures and binding energies in DNA structures. Our xTB values for DNA base binding energy were in the same order and in some cases better than CAM-B3LYP values compared to experimental values. Double-stranded DNA-cisplatin structures have been calculated and the hydrogen bonds of water molecules are a decisive factor contributing to the preference for the cisplatin-Guanine interaction. Higher values of the water hydrogen bonding energies were obtained in cisplatin-Guanine structures. Furthermore, the electrostatic potential was used to investigate and improve the analysis of DNA-cisplatin structures. We applied the xTB method and the CAM-B3LYP functional combined with def2-SVP basis set to perform and analyze of the bonding energies of the cisplatin interaction and the effects of the hydrogen bonds. Results were calculated employing the xTB and the ORCA software.

Enhanced photoluminescence characteristics in Mg doped Alq3: An insight into doping mechanism

The present paper deals with the investigations on the effect of Mg doping on the structural and photophysical properties of Alq3 thin films. Mg doped Alq3 powders, with varying Mg concentrations, are synthesized using co-precipitation method and their thin films are deposited using vacuum evaporation method. These films are subjected to different analytical analyses to study the effect of Mg doping on the structural and photophysical properties of Alq3. It has been observed that Mg is attached at the central part of the Alq3 molecules making bonds with Al, N and O atoms. In this process, Mg atoms transfer electrons to Alq3 molecules and increases the electron density in its highest occupied molecular orbital (HOMO). Increased HOMO electron density in Mg doped Alq3 results in the improvement in its photoluminescence characteristics. Highest photoluminescent characteristics are observed for Mg doped Alq3 having 1.5 % (by mole) Mg which shows almost 2-fold enhancement in photoluminescence quantum efficiency (PLQY) and 3-fold enhancement in radiative decay rate. The results obtained in this work suggest that Mg doped Alq3 films may be integrated in high performing organic light emitting devices.

Insight into Cr Alloying on Face‐Centered Cubic to Body‐Centered Cubic Phase Transition in FeCr Alloy

Effects of Cr alloying on phase stability, magnetism, and electronic structures in both body‐centered cubic (bcc) and face‐centered cubic (fcc) phases and on the transformation from fcc to bcc are studied by first‐principles calculations. Results show that the doped Cr atoms in fcc and bcc phases choose distinct occupation models. This phenomenon can be understood from the amount of electron density of states close to Fermi energy. For magnetism, Cr tends to be antiferromagnetically coupled with the surrounding Fe in the studied phases. The magnetic moment of Fe is greater than that of Cr in bcc, but the order is reversed in fcc. The moment of Fe is dictated by the distance between it and the doped Cr in bcc, whereas it is dominated by spatial orientation with Cr in fcc. For phase stability, it is found that the alloying of Cr prefers destabilizing bcc while tends to stabilize fcc, leading to a strong inhibition of phase transition from fcc to bcc. Notably, the role in the fcc phase is more prominent than that in bcc, which can be associated with the antiferromagnetism between Fe and Cr in fcc.

Effect of the behavior on direct–indirect electronic transitions of SrZrO3 nanowires grown in the crystallographic directions [100] and [110]: Ab-initio study

In the present work, we studied a set of strontium zirconate nanowires of different diameters oriented in the directions [100] and [110]. The density functional theory calculations were performed using the quantum espresso code, which confidently employs a combination of plane waves. In this study, we utilized a pseudopotential proposed by Perdew, Burke, and Ernzerhof to model the exchange–correlation energy using a generalized gradient approximation. In the study’s first phase, we performed a structural optimization of the nanowires by adjusting the atomic positions and lattice parameters. After calculating the electronic band structure and density of states, we found that the strontium zirconate nanowires in this study are semiconductors. The nanowires in the [100] direction have an indirect transition, while those in the [110] direction have a direct transition. Besides, the bandgap varies with diameter. We also calculated the density of states projected. Based on the results, it can be observed that the p orbital of oxygen is the primary contributor to the density of states in the valence region. On the other hand, in the conduction region, the density of states is mainly affected by the d and s orbitals of zirconium. Due to their exceptional electronic properties, strontium zirconate nanowires are up-and-coming candidates for photocatalysis and solar cell applications.

Ultra‐Small Au Nanoclusters with Tailored Photoluminescence Properties using Modified Thiol Ligands: A Computational and Experimental Demonstration

AbstractAu nanoclusters with tailored photoluminescence can be obtained through controlled nanoparticle ligand interface chemistry. The present work reports molecular gold nanoclusters with tuneable photoluminescence emission from 600 to 700 nm using N,N′,N″‐trialkyl (11‐mercaptoundecyl)ammonium chloride ligands as capping‐agents. The tunability within red spectral region is regulated through specific interface chemistry between gold nanoclusters of molecular range and functional groups of the quaternary ammonium head over N,N′,N″‐trialkyl(11‐mercaptoundecyl)ammonium chloride. Combined understanding obtained from the spectroscopy, microscopy, and density functional theory studies demonstrate that the functional group specific electronic interactions at the interfaces steer the emission characteristics of “molecular” Au nanoparticles. The study clearly identifies that bulkier functional groups, i.e., triethyl, tripropyl, tributyl, and dimethyl benzene over N+ (of thiol ligand) through their steric effects minimize the particle size giving rise to tunable photoluminescence emission in red spectral region. However, the red shift seen in the emission Au nanoclusters with N‐(11‐mercaptoundecyl)‐N,N′‐dimethylbenzenammonium chloride ligand in contradiction to particle size effect is computationally proved to be due to the delocalization of electron density from benzene aromatic ring to N+ of ammonium head leading to a reduction in the HOMO‐LUMO energy gap.

Bifurcation analysis of electron-acoustic waves in electron beam-plasma with suprathermal electrons

It has investigated the properties of nonlinear electron-acoustic waves propagating in a four-component collisionless, unmagnetized plasma. The system consists of cool inertial background electrons of temperature T c , the cool inertial electron beam of temperature T b , hot inertialess suprathermal electrons modeled by a κ-distribution of temperature T h , and ions. The nonlinear modified Korteweg-de Vries-Burgers (mKdV-Burgers) equation that characterizes the electron acoustic waves in such a plasma model is derived. The wave solutions of the resultant mKdV-Burgers equation are investigated using planar dynamical system bifurcation theory. The unperturbed hot, cool, and beam electron densities and the superthermal electron parameter are revealed to have a considerable influence on the nonlinear electron-acoustic traveling waves and the associated electric fields. The system evolves also monotonic shock waves when the dissipation term dominates over the dispersion term. The current model might be useful for understanding the generation of nonlinear electron-acoustic waves in a variety of astrophysical plasma settings, including the Earth's magnetosphere.

Atropisomeric Properties of 5N‐Benzoyl‐1,5‐benzodiazepin‐2‐ones: Substituent Effects on Rotation around the Ar−N(CO) Axis

Abstract5N‐Benzoyl‐1,5‐benzodiazepin‐2‐ones with various substituents were synthesized and their atropisomeric properties were analyzed. For the rotational isomers (E/Z) based on the amide bond [N−C(=O)], the E‐isomers were preferentially formed regardless of the substituents. Atropisomers (aR/aS) due to the Ar−N(CO) (sp2‐sp2) axis were isolated using chiral HPLC, and the rotational barrier (ΔG≠) in thermal isomerization was measured. The rotation barrier about the Ar−N(CO) axis was affected by both the substituents at the C6‐position and the p‐substituents on the benzoyl group. The substituents at C6 (R1) caused both steric and electronic effects. On the other hand, the p‐substituents (R2) on the benzoyl group caused electronic effects: the electron‐donating group (EDG) lowered the ΔG≠ value, whereas the electron‐withdrawing group (EWG) raised it. The ΔG≠ values were linearly correlated with the magnitude of the electronic effect (Hammett σ constants) of functional groups (R2). The EDG causes an increase in the electron density on the carbonyl moiety in the amide, which may disturb the planarity of the amide bond, resulting in a decrease in the ΔG≠ value.

Drag of electron-hole bilayer in silicon-on-insulator metal-oxide-semiconductor field-effect transistor at low temperature

Abstract Drag between the electron-layer and the hole-layer formed in a silicon-on-insulator metal-oxide-semiconductor field-effect-transistor, with the estimated interlayer distance as small as 18 nm, is investigated. The drag resistance is measured at 10 K and mapped on the plane defined by the electron density and hole density. The analysis shows that the Coulomb drag predominates over the competing virtual-phonon drag. The observed drag resistance is as large as 103 - 104 Ω, indicating strong Coulomb interaction between the electron and hole layers.

Structure and dynamics of the Hermean magnetosphere revealed by electron observations from the Mercury electron analyzer after the first three Mercury flybys of BepiColombo

The Mercury electron analyzer (MEA) obtained new electron observations during the first three Mercury flybys by BepiColombo on October 1, 2021 (MFB1), June 23, 2022 (MFB2), and June 19, 2023 (MFB3). BepiColombo entered the dusk side magnetotail from the flank magnetosheath in the northern hemisphere, crossed the Mercury solar orbital equator around midnight in the magnetotail, traveled from midnight to dawn in the southern hemisphere near the closest approach, and exited from the post-dawn magnetosphere into the dayside magnetosheath. We aim to identify the magnetospheric boundaries and describe the structure and dynamics of the electron populations observed in the various regions explored along the flyby trajectories. We derive 4s time resolution electron densities and temperatures from MEA observations. We compare and contrast our new BepiColombo electron observations with those obtained from the Mariner 10 scanning electron spectrometer (SES) 49 years ago. A comparison to the averaged magnetospheric boundary crossings of MESSENGER indicates that the magnetosphere of Mercury was compressed during MFB1, close to its average state during MFB2, and highly compressed during MFB3. Our new MEA observations reveal the presence of a wake effect very close behind Mercury when BepiColombo entered the shadow region, a significant dusk-dawn asymmetry in electron fluxes in the nightside magnetosphere, and strongly fluctuating electrons with energies above 100s eV in the dawnside magnetosphere. Magnetospheric electron densities and temperatures are in the range of 10-30 cm$^ $ and above a few 100s eV in the pre-midnight-sector, and in the range of 1-100 cm$^ $ and well below 100 eV in the post-midnight sector, respectively. The MEA electron observations of different solar wind properties encountered during the first three Mercury flybys reveal the highly dynamic response and variability of the solar wind-magnetosphere interactions at Mercury. A good match is found between the electron plasma parameters derived by MEA in the various regions of the Hermean environment and similar ones derived in a few cases from other instruments on board BepiColombo.