Charge Density Properties Research Articles

Effect of B–Si bond charge density on the structural and elastic properties of silicene

Single-atomic boron-silicon (B–Si) layers show promise for applications in the field of two dimensional (2D) electronic devices. Using density functional theory, we have estimated the charge density properties along the various directions in 2D B–Si compounds. We have found that the Young’s modulus for B-doped silicene increases in two mutually perpendicular ‘armchair’ and ‘zigzag’ deformation directions. We show that the increase in Young’s modulus occurs due to the electron density increase on the B–Si bond.

Combined quantum mechanics/molecular mechanics (QM/MM) methods to understand the charge density distribution of estrogens in the active site of estrogen receptors.

The ligand binding to protein and host–guest interactions are ubiquitous for molecular recognition. In drug design, the ligand binding to the active site of proteins is influenced by the charge density distribution and the electrostatic interactions of ligands and the nearby amino acids of the protein. The charge density analyses of ligand–protein complexes need accurate positions of hydrogen atoms and their valence electron distribution and the fine structure of proteins. Such information cannot be obtained from the conventional protein X-ray crystallography analysis in the resolution range of 1.5 to 3.5 Å. This can be realized from QM/MM based structure and charge density analysis of estrogens with the estrogen receptor. The charge density properties such as electron density, Laplacian of electron density and electrostatic properties of estrogens in the presence of active site amino acid residues have been determined and compared with the isolated estrogen molecules from theory and experimental. The present study reveals the chemical bonding nature of estrogen molecules and the strength of the intermolecular interactions in the active site of estrogen receptor, and also the importance of π⋯π interactions between the estrogens and Phe404 amino acid residue and protonation state of His524 amino acid residue have been identified using electrostatic potential maps. The difference in the electrostatic potential map of estrogens displays the hormone dependent actions of estrogen receptor. This method is very helpful to derive the charge density distribution of macromolecules to understand their biological recognition and interactions.

Acylguanidine-BACE1 complex: Insights of intermolecular interactions and dynamics

Alzheimer disease (AD) is a harmful neurodegenerative disorder which arises mainly due to awful deposition of amyloid β (Aβ) peptide in the brain of AD patients. Aβ aggregates from the amyloid precursor protein (APP) by the sequential action of β-Secretase (Beta site APP Cleaving Enzyme, BACE1); hence, inhibition of BACE1 is the primary target for the treatment of AD. As per the experimental report, acylguanidine is a synthetic inhibitor of BACE1, it exhibits high binding affinity towards BACE1. In the present computational study, we aimed to understand the molecular binding mechanism of acylguanidine with BACE1 from the structure and conformation, intermolecular interactions, charge density and electrostatic properties, stability and binding free energy of acylguanidine molecule in the active site of BACE1. To investigate this, molecular docking, QM/MM based charge density analysis and MD simulation have been performed on acylguanidine with BACE1. Acylguanidine shows large binding affinity towards BACE1 and it gives strong hydrogen bonding and hydrophobic interactions with the active site amino acid residues of BACE1. In addition, QM/MM based charge density analysis of acylguanidine was carried out to understand its charge density distribution in the active site of BACE1. The conformational flexibility, charge density redistribution and the modification of electrostatic properties of acylguanidine in the active site have been compared to its corresponding gas phase structure. Further, the molecular dynamics simulation on acylguanidine-BACE1 was carried out, which gives the stability of acylguanidine in the active site of BACE1. The MM-GBSA free energy displays the binding affinity of the acylguanidine and further the decomposition energy reveals the validity of intermolecular interactions.

Calcium Orthophosphate (CaPO4) Scaffolds for Bone Tissue Engineering Applications

The chemical and structural similarities of calcium orthophosphates (abbreviated as CaPO4)to the mineral composition of natural bones and teeth have made them a good candidate for bone tissue engineering applications. Nowadays, a variety of natural or synthetic CaPO4-based biomaterials is produced and has been extensively used for dental and orthopedic applications. Despite their inherent brittleness, CaPO4 materials possess several appealing characteristics as scaffold materials. Namely, their biocompatibility and variable stoichiometry, thus surface charge density, functionality and dissolution properties, make them suitable for both drug and growth factor delivery. Therefore, CaPO4, especially hydroxyapatite (HA) and tricalcium phosphates (TCPs), have attracted a significant interest in simultaneous use as bone grafts and drug delivery vehicles. Namely, CaPO4-based three-dimensional (3D) scaffolds and/or carriers have been designed to induce bone formation and vascularization. These scaffolds are usually porous and harbor various types of drugs, biologically active molecules and/or cells. Over the past few decades, their application as bone grafts in combination with stem cells has gained much importance. This review discusses the source, manufacturing methods and advantages of using CaPO4 scaffolds for bone tissue engineering applications. Perspective future applications comprise drug delivery and tissue engineering purposes.

Novel Conducting and Biodegradable Copolymers with Noncytotoxic Properties toward Embryonic Stem Cells.

Electroactive biomaterials that are easily processed as scaffolds with good biocompatibility for tissue regeneration are difficult to design. Herein, the synthesis and characterization of a variety of novel electroactive, biodegradable biomaterials based on poly(3,4-ethylenedioxythiphene) copolymerized with poly(d,l lactic acid) (PEDOT-co-PDLLA) are presented. These copolymers were obtained using (2,3-dihydrothieno[3,4-b][1,4]dioxin-2-yl)methanol (EDOT-OH) as an initiator in a lactide ring-opening polymerization reaction, resulting in EDOT–PDLLA macromonomer. Conducting PEDOT-co-PDLLA copolymers (in three different proportions) were achieved by chemical copolymerization with 3,4-ethylenedioxythiophene (EDOT) monomers and persulfate oxidant. The PEDOT-co-PDLLA copolymers were structurally characterized by 1H NMR and Fourier transform infrared spectroscopy. Cyclic voltammetry confirmed the electroactive character of the materials, and conductivity measurements were performed via electrochemical impedance spectroscopy. In vitro biodegradability was evaluated using proteinase K over 35 days, showing 29–46% (w/w) biodegradation. Noncytotoxicity was assessed by adhesion, migration, and proliferation assays using embryonic stem cells (E14.tg2a); excellent neuronal differentiation was observed. These novel electroactive and biodegradable PEDOT-co-PDLLA copolymers present surface chemistry and charge density properties that make them potentially useful as scaffold materials in different fields of applications, especially for neuronal tissue engineering.

DONNAN DIALYSIS ASSISTED BY INTERPENETRATING POLYMER NETWORKS FOR CHROMIUM ION TRANSPORT IN AQUEOUS MEDIA

Macroporous polypropylene (MPP) membranes incorporating poly[sodium (styrene sulphonate)], P(SSNa), and poly[(ar-vinylbenzyl) trimethylammonium chloride],P(ClVBTA) were modified via “in situ” radical polymerization. Modified and unmodified MPP were characterized using SEM and charge density properties. Donnan dialysis was used to transport chromium ions. The results show that the degree of modification varied between 2.5% and 4.0%, and the water uptake percentage varied between 15% and 20%. Experimental data for chromium ion transport (Cr(III) and Cr(VI)) were fitted to a mathematical model, and a correlation coefficient very close to 1 was obtained. The main parameters of this mathematical fit are k and a. These parameters report the concentration of chromium ions that converge in the Donnan equilibrium (k) and the response rate of the modified membrane (a).

The effect of anion-π interactions on the properties of pyrazinamide and some related compounds

The effects of anion-π interaction on the protonation tendency and amide functional group properties of pyrazinamide (PZA) and related compounds have been investigated by the quantum mechanical methods. The pyrazine ring were replaced by pyrimidine and triazine rings in order to investigate the effect of second and third nitrogen heteroatoms and their positions on the amide functional group. The increase in the number of nitrogen heteroatoms of the ring rises the anion-π interaction energy. Thermodynamic properties calculated in the water solvent by the SCRF continuum solvation method using the IEF-PCM model, confirm the decrease in the proton affinity and basicity with solvation, while the anion-π interactions increase those in both gas phase and solvation media. The effect of anion type, via the anion-π interaction, on the basicity is approximately negligible. Well-defined relations are established between the anion-π interaction energies ΔE and the valence natural orbital energies ∑NAO of protonated site, charge transfer between two units and the minimum value of electrostatic potential Vmin around the oxygen atom. In addition, linear relationships are observed between the ΔE value and the distance between anion and the center of heterocyclic ring (ranion···π), the topological properties of electron charge density ρ and the 1H NMR absolute shielding constant (δ1 H) of proton. In agreement with the ΔE changes, the effects of second and third heteroatoms are additive on the charge transfer Δq, |∑NAO| and proton affinity.

Theoretical Study of the Structural, Electronic, Chemical Bonding and Optical Properties of the A21 am Orthorhombic SrBi2Ta2O9

The structural parameters, density of states, electronic band structure, charge density, and optical properties of orthorhombic SrBi2Ta2O9 have been investigated using the plane-wave ultrasoft pseudopotential technique based on the first-principle density functional theory (DFT). The calculated structural parameters were in agreement with the previous theoretical and experimental data. The band structure showed an indirect (S to Γ) band gap with 2.071 eV. The chemical bonding along with population analysis has been studied. The complex dielectric function, refractive index, and extinction coefficient were calculated to understand the optical properties of this compound, which showed an optical anisotropy in the components of polarization directions (100), (010), and (001).

Adsorption of acetylene on ordered NixAg1-x/Ni (111) and effect of Ag-dopant: A DFT study

The adsorption of acetylene molecules on the ordered NixAg1-x/Ni (111) (x = 1, 0.75, 0.5, 0.25) bimetallic surfaces was investigated by using the density functional theory (DFT). Among the model systems, Ni atom was replaced by Ag atom only on the top surface layer. The results show that, as the Ag concentration increases, the interaction between Ag-modified NixAg1-x/Ni (111) and acetylene molecules decreases gradually. Additionally, the adsorption processes of acetylene molecules on different considered surfaces are all exothermic thermodynamically. Furthermore, the Partial density states (PDOS) and the differential charge density properties suggest that an increase in atomic concentration of Ag in the upmost layer decreases the electron transfer between the acetylene molecule and surface. Our results could provide useful information to increase the activity of Ni-based catalysts for acetylene hydrogenation.

Determination of chemical identity and occupancy from experimental density maps.

Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity-based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B-factor in Fourier transforms of the corresponding maps. An application of this theory is described to an experimental ED map at 1.73-Å resolution, and to an experimental CD map at 2.2-Å resolution. All the three density functions are linearly proportional to occupancy when the structure factor F(000) term of Fourier transforms of experimental density maps is included. Upon application of this theory to both experimental CD and ESP maps recently reported for photosystem II-light harvesting complex II supercomplex at 3.2-Å resolution, the occupancy of two extrinsic protein subunits PsbQ and PsbP is determined to be 20.4 ± 0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein α-helices.

Synthesis, crystal structure, optical property and theoretical studies of a noncentrosymmetric telluromolybdate CoTeMoO6

Polycrystalline CoTeMoO6 has been synthesized, and CoTeMoO6 crystals have been grown by spontaneous crystallization. Band structure, density of states, charge density, electronic structures and optical properties of CoTeMoO6 crystal were calculated by using a first-principles method for the first time. Optical and nonlinear optical properties of CoTeMoO6 crystal were measured. Structure and charge density analyses indicate that cleavage maybe exist in CoTeMoO6 crystal. The experiment results of optical properties show that a strong absorption band exhibits at 458–692 nm in the visible region. The absorption band plays an important role in the coloration of CoTeMoO6 crystal. The SHG responses of CoTeMoO6 with a 1.06 μm laser is much weaker than that of KDP, which can be ascribed to the absorption band caused by spin-allowed d-d transitions of Co2+ ions. Thus CoTeMoO6 crystal is not suited to be used as nonlinear optical material in the Vis-NIR region.

The influence of correlation effects on the electronic structure of double-decker bis(phthalocyaninato)-Dy, Tb complexes

By using DFT+U approach, we investigated the influence of the electronic correlation in the 4f manifold of lanthanide atom upon the electronic structure of double-decker bis(phthalocyaninato)-Dy, Tb complexes. We monitored the density of states, electronic populations and charge density properties in the framework of Hubbard U and J values, highlighting the different electronic behaviour of the two phthalocyanine units. Our results show that important changes occurs at the level of electronic populations, while the density of states of nitrogen atoms display only small changes, restricted to a specific energy window. We also emphasized the mechanisms connecting these changes to the geometric structure of the complexes. Finally, the dependence between possible spin communication channels and the strength of correlation in double-decker -Dy and -Tb molecules was examined.

Structure and Charge Density Properties of (1 − x)(Na1−y K y NbO3)-xBaTiO3 Lead-Free Ceramic Solid Solution

(1 − x)(Na1−yKy)NbO3-xBaTiO3 (abbreviated as NKN-BT, x = 0.1, 0.2; y = 0.01, 0.05) ceramics were synthesized by the solid-state reaction method. Powder x-ray diffraction analysis in combination with the profile refinement method was employed for quantitative phase analysis and structural refinement. The x-ray diffraction study shows that phase transition occurs from tetragonal to distorted cubic with the compositions between x = 0.1 and x = 0.2. The spatial arrangements of the electron distribution and bonding nature of the samples have been analyzed through the maximum entropy method. The optical band gap energy of the prepared solid solutions has been determined using UV-visible spectrophotometry. The optical band gap energy of the solid solutions decreases with the increase in BaTiO3 content. The elemental composition of these ceramics has been studied using energy dispersive x-ray analysis and the microstructure has been examined by scanning electron microscopy. The piezoelectric coefficient (d33) measurement of the ceramics shows the enhancement of piezoelectric properties in the tetragonal phase. The maximum value of the piezoelectric coefficient (d33) obtained for the solid solution is 120 pC/N. With increasing BaTiO3 content in the solid solutions, the ferroelectric behavior weakens.

N-Co共掺锐钛矿相TiO2光学性质的第一性原理研究

The electronic structures, deformation charge density, dipole moment, and optical properties of N-La-codoped anatase titanium dioxide (TiO2) are studied using the plane-wave ultrasoft pseudopotential method based on the density functional theory (DFT). The optical properties of two-ion-doped TiO2 are analyzed via electronic structures, deformation charge density, and dipole moment. For the model of N-La-doped TiO2 , a smaller atom fraction of N and La atoms induces better optical properties. The absorption edges of two doped TiO2 models redshift to the visible-light region.

Theoretical Investigation of Electronic Properties of Undoped and Ag-Doped (CdTe)16×N Multi-cage Nanochains

The structural and electronic properties of highly stable structures, undoped and Ag substitutional doped (CdTe)16×N (N = 1–3) multi-cage nanochains, have been investigated by density functional theory. (CdTe)16 cage is chosen as the building unit to form (CdTe)16×N multi-cage nanochains. Two possible assembly modes, interconnecting two cages by their four-membered rings and interconnecting two cages by their six-membered rings, are considered. For Ag doping, two different substitutional sites have been studied. Our results show that the multi-cage nanochains have higher stability than that of the single cage, and the stability varies with the assembly modes and doping sites for both undoped and Ag-doped nanochains. After Ag doping, an acceptor level is observed, showing typical p-type properties. The properties of energy structure, charge density and density of states are analyzed in detail. Results show that the assembly modes and Ag substitutional doping site have a significant impact on the electronic properties of Ag-doped (CdTe)16×N multi-cage nanochains.

Charged Triazole Cross-Linkers for Hyaluronan-Based Hybrid Hydrogels.

Polyelectrolyte hydrogels play an important role in tissue engineering and can be produced from natural polymers, such as the glycosaminoglycan hyaluronan. In order to control charge density and mechanical properties of hyaluronan-based hydrogels, we developed cross-linkers with a neutral or positively charged triazole core with different lengths of spacer arms and two terminal maleimide groups. These cross-linkers react with thiolated hyaluronan in a fast, stoichiometric thio-Michael addition. Introducing a positive charge on the core of the cross-linker enabled us to compare hydrogels with the same interconnectivity, but a different charge density. Positively charged cross-linkers form stiffer hydrogels relatively independent of the size of the cross-linker, whereas neutral cross-linkers only form stable hydrogels at small spacer lengths. These novel cross-linkers provide a platform to tune the hydrogel network charge and thus the mechanical properties of the network. In addition, they might offer a wide range of applications especially in bioprinting for precise design of hydrogels.

Electrochemical analysis of single particles

Nanoparticles (NPs) have attracted much more attention over the past two decades because of their various applications in both fundamental aspects and industrial applications. In this context, development of new techniques to detect and study single NP behavior is of significant importance because the function of NP is closely related to its size, morphology, surface charge density and chemical properties. Electrochemical techniques have made a great contribution to investigating on the single nanoparticle properties (e.g., surface charge, geometry, and surface chemistry) over the past ten years. This review focuses on the recent progress on single particles analysis with electrochemical techniques that are classified into three categories based on the detection principles, i.e., nanoparticle-microelectrode collision, resistive-pulse analysis and other electrochemical-based methods.

Effects of Al-Impurity Type on Formation Energy, Crystal Structure, Electronic Structure, and Optical Properties of ZnO by Using Density Functional Theory and the Hubbard-U Method.

We systematically investigated the effects of Al-impurity type on the formation energy, crystal structure, charge density, electronic structure, and optical properties of ZnO by using density functional theory and the Hubbard-U method. Al-related defects, such as those caused by the substitution of Zn and O atoms by Al atoms (Als(Zn) and Als(O), respectively) and the presence of an interstitial Al atom at the center of a tetrahedron (Ali(tet)) or an octahedron (Ali(oct)), and various Al concentrations were evaluated. The calculated formation energy follows the order Ef(Als(Zn)) < Ef(Ali(tet)) < Ef(Ali(oct)) < Ef(Als(O)). Electronic structure analysis showed that the Als(Zn), Als(O), Ali(tet), and Ali(oct) models follow n-type conduction, and the optical band gaps are higher than that of pure ZnO. The calculated carrier concentrations of the Als(O) and Ali(tet)/Ali(oct) models are higher than that of the Als(Zn) model. However, according to the curvature of the band structure, the occurrence of interstitial Al atoms or the substitution of O atoms by Al atoms results in a high effective mass, possibly reducing the carrier mobility. The average transmittance levels in the visible light and ultraviolet (UV) regions of the Als(Zn) model are higher than those of pure ZnO. However, the presence of an interstitial Al atom within the ZnO crystal reduces transmittance in the visible light region; Als(O) substantially reduces the transmittance in the visible light and UV regions. In addition, the properties of ZnO doped with various Als(Zn) concentrations were analyzed.

Recent developments in the ABINIT software package

ABINIT is a package whose main program allows one to find the total energy, charge density, electronic structure and many other properties of systems made of electrons and nuclei, (molecules and periodic solids) within Density Functional Theory (DFT), Many-Body Perturbation Theory (GW approximation and Bethe–Salpeter equation) and Dynamical Mean Field Theory (DMFT). ABINIT also allows to optimize the geometry according to the DFT forces and stresses, to perform molecular dynamics simulations using these forces, and to generate dynamical matrices, Born effective charges and dielectric tensors. The present paper aims to describe the new capabilities of ABINIT that have been developed since 2009. It covers both physical and technical developments inside the ABINIT code, as well as developments provided within the ABINIT package. The developments are described with relevant references, input variables, tests and tutorials. Program summaryProgram title: ABINITCatalogue identifier: AEEU_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEU_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, version 3No. of lines in distributed program, including test data, etc.: 4845789No. of bytes in distributed program, including test data, etc.: 71340403Distribution format: tar.gzProgramming language: Fortran2003, PERL scripts, Python scripts.Classification: 7.3, 7.8.External routines: (all optional) BigDFT [2], ETSF_IO [3], libxc [4], NetCDF [5], MPI [6], Wannier90 [7], FFTW [8].Catalogue identifier of previous version: AEEU_v1_0Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 2582Does the new version supersede the previous version?: Yes. The abinit-7.10.5 version is now the up to date stable version of ABINITNature of problem:This package has the purpose of computing accurately material and nanostructure properties: electronic structure, bond lengths, bond angles, primitive cell size, cohesive energy, dielectric properties, vibrational properties, elastic properties, optical properties, magnetic properties, non-linear couplings, electronic and vibrational life-times, and others.Solution method:Software application based on Density Functional Theory, Many-Body Perturbation Theory and Dynamical Mean Field Theory, pseudopotentials, with plane waves or wavelets as basis functions.Reasons for new version:Since 2009, the abinit-5.7.4 version of the code has considerably evolved and is not yet up to date. The abinit- 7.10.5 version contains new physical and technical features that allow electronic structure calculations impossible to carry out in the previous versions.Summary of revisions:•new physical features: quantum effects for the nuclei treated by the Path-integral Molecular Dynamics; finding transition states using image dynamics (NEB or string methods); two component DFT for electron-positron annihilation; linear response in a Projector Augmented-Wave approach -PAW-, electron-phonon interactions and temperature dependence of the gap; Bethe Salpeter Equation -BSE-; Dynamical Mean Field Theory (DMFT).•new technical features: development of a PAW approach for a wavelet basis; parallelisation of the code on more than 10,000 processors; new build system.•new features in the ABINIT package: tests; test farm; new tutorials; new pseudopotentials and PAW atomic data tables; GUI and postprocessing tools like the AbiPy and APPA libraries.Running time:It is difficult to answer to the question as the use of ABINIT is very large. On one hand, ABINIT can run on 10,000 processors for hours to perform quantum molecular dynamics on large systems. On the other hand, tutorials for students can be performed on a laptop within a few minutes.

The role of allophane nano-structure and Fe oxide speciation for hosting soil organic matter in an allophanic Andosol

We evaluated the impact of nano-structural characteristics of allophanic compounds and Fe oxide speciation on the efficiency of organo-mineral interactions in an allophanic Andosol derived from volcanic ash (Eifel mountains, Germany). The samples selected for our work represented a gradient from: (i) a pure synthetic allophane and (ii) model organo-mineral mixtures to (iii) particle size fractions of the natural Andosol. We thus aimed to link the processes operating at the individual molecular scale to the phenomena active at the aggregate scale. For a non-destructive characterization of the samples, we applied 129Xe NMR spectroscopy of adsorbed Xe atoms (to identify the mineral nano-structure and surface acid centres), ESEM (verifying the nano-spherical structure of allophane), 13C CPMAS NMR (for the nature of the soil organic matter (SOM)), 57Fe Mössbauer spectroscopy (Fe oxide speciation), and N2 adsorption (contribution of micro- and mesoporosity). By using the atomic probe Xe, we obtained evidence for a coupled mechanism of adsorption onto allophane requiring both the narrow pores (voids formed by the primary nano-spherules) and the acid centres located at the defect surfaces of the primary spherules. The validity of this coupled mechanism for the sorption of organic matter was confirmed by the concomitant blocking of acid centres (129Xe NMR data) and the decrease of the N2-available pore volumes (Vmicro and Vmeso) in the model samples DOM/- and NOM/allophane (DOM=dissolved OM, NOM=natural OM). In the Andosol, the high resistance of SOM against oxidation (OCresist=15–50%) was combined with preferential accumulation of certain organic compounds, e.g. potentially labile substrates such as carbohydrates, and the low molecular weight species such as amino acids. This feature was attributed to the peculiar microporous tortuous structure of allophane aggregates that likely impose certain criteria for the chemical nature and size of mineral-bound SOM. On the other hand, the revealed dominance of nanoparticulate Fe oxyhydroxides (57% ferrihydrite) and Fe-substituted allophane (supposedly formed due to co-precipitation of the Al, Si and Fe in the course of volcanic soil formation) may substantially contribute to the formation of highly resistant organo-mineral associations through the enhanced extent of reactive surface groups in nanoparticles, increased surface charge density and electron accepting properties of substituting Fe3+ species that supposedly enhance the proportion of oxidised organic components.