Charge Density Analysis Research Articles

Towards understanding π-stacking interactions between non-aromatic rings.

The first systematic study of π interactions between non-aromatic rings, based on the authors' own results from an experimental X-ray charge-density analysis assisted by quantum chemical calculations, is presented. The landmark (non-aromatic) examples include quinoid rings, planar radicals and metal-chelate rings. The results can be summarized as: (i) non-aromatic planar polyenic rings can be stacked, (ii) interactions are more pronounced between systems or rings with little or no π-electron delocalization (e.g. quinones) than those involving delocalized systems (e.g. aromatics), and (iii) the main component of the interaction is electrostatic/multipolar between closed-shell rings, whereas (iv) interactions between radicals involve a significant covalent contribution (multicentric bonding). Thus, stacking covers a wide range of interactions and energies, ranging from weak dispersion to unlocalized two-electron multicentric covalent bonding ('pancake bonding'), allowing a face-to-face stacking arrangement in some chemical species (quinone anions). The predominant interaction in a particular stacked system modulates the physical properties and defines a strategy for crystal engineering of functional materials.

First-principles study on OH-functionalized 2D electrides: Ca2NOH and Y2C(OH)2, promising two-dimensional monolayers for metal-ion batteries

We designed two stable monolayers of Ca2NOH and Y2C(OH)2 through replacing the anionic electrons with negatively charged hydroxide ions. Calculation results indicate that these two monolayers are dynamic and thermodynamic stable. Ca2NOH is determined as an indirect semiconductor with band gap of 1.51 eV based on hybrid functional calculations, while Y2C(OH)2 possesses a direct band gap of 0.72 eV. Moreover, to investigate the potential applications of Ca2NOH and Y2C(OH)2 monolayers, we studied the adsorption and diffusion performance of Li, Na and Mg atoms on their surfaces. The calculated adsorption energies, differential charge density and Bader charge analysis reveal that Li, Na and Mg atoms could anchor on Ca2NOH and Y2C(OH)2 surfaces. Nudged Elastic band calculation results suggest that the barriers for Li, Na, and Mg diffusion on Ca2NOH surface are 0.79 eV, 0.42 eV and 0.42 eV. While Y2C(OH)2 monolayer exhibits relative low diffusion barriers of 0.60 eV, 0.26 eV and 0.10 eV for Li, Na and Mg, respectively and their corresponding diffusion coefficients are as large as 1.52 × 10−18, 1.52 × 10−12 and 1.52 × 10−8 m2/s. The diffusion barriers and diffusion coefficients. The appropriate adsorption energies, low diffusion barriers and relative large diffusion coefficients of Na/Mg atoms imply that Ca2NOH and Y2C(OH)2 monolayers are promising electrode materials for the corresponding metal-ion batteries. All the results serves to modify, stabilize and understand two dimensional electrides and put their properties into practical use.

Tin, The Enabler-Hydrogen Diffusion into Ruthenium.

Hydrogen interaction with ruthenium is of particular importance for the ruthenium-capped multilayer reflectors used in extreme ultraviolet (EUV) lithography. Hydrogen causes blistering, which leads to a loss of reflectivity. This problem is aggravated by tin. This study aims to uncover the mechanism via which tin affects the hydrogen uptake, with a view to mitigation. We report here the results of a study of hydrogen interaction with the ruthenium surface in the presence of tin using Density Functional Theory and charge density analyses. Our calculations show a significant drop in the energy barrier to hydrogen penetration when a tin atom or a tin hydride molecule (SnHx) is adsorbed on the ruthenium surface; the barrier has been found to drop in all tested cases with tin, from 1.06 eV to as low as 0.28 eV in the case of stannane (SnH4). Analyses show that, due to charge transfer from the less electronegative tin to hydrogen and ruthenium, charge accumulates around the diffusing hydrogen atom and near the ruthenium surface atoms. The reduced atomic volume of hydrogen, together with the effect of electron–electron repulsion from the ruthenium surface charge, facilitates subsurface penetration. Understanding the nature of tin’s influence on hydrogen penetration will guide efforts to mitigate blistering damage of EUV optics. It also holds great interest for applications where hydrogen penetration is desirable, such as hydrogen storage.

Significance of hydrogen bonding and other noncovalent interactions in determining octahedral tilting in the CH3NH3PbI3 hybrid organic-inorganic halide perovskite solar cell semiconductor

The CH3NH3PbI3 (methylammonium lead triiodide) perovskite semiconductor system has been viewed as a blockbuster research material during the last five years. Because of its complicated architecture, several of its technological, physical and geometrical issues have been examined many times. Yet this has not assisted in overcoming a number of problems in the field nor in enabling the material to be marketed. For instance, these studies have not clarified the nature and type of hydrogen bonding and other noncovalent interactions involved; the origin of hysteresis; the actual role of the methylammonium cation; the nature of polarity associated with the tetragonal geometry; the unusual origin of various frontier orbital contributions to the conduction band minimum; the underlying phenomena of spin-orbit coupling that causes significant bandgap reduction; and the nature of direct-to-indirect bandgap transition features. Arising from many recent reports, it is now a common belief that the I···H–N interaction formed between the inorganic framework and the ammonium group of CH3NH3+ is the only hydrogen bonded interaction responsible for all temperature-dependent geometrical polymorphs of the system, including the most stable one that persists at low-temperatures, and the significance of all other noncovalent interactions has been overlooked. This study focussed only on the low temperature orthorhombic polymorph of CH3NH3PbI3 and CD3ND3PbI3, where D refers deuterium. Together with QTAIM, DORI and RDG based charge density analyses, the results of density functional theory calculations with PBE with and without van der Waals corrections demonstrate that the prevailing view of hydrogen bonding in CH3NH3PbI3 is misleading as it does not alone determine the a−b+a− tilting pattern of the PbI64− octahedra. This study suggests that it is not only the I···H/D–N, but also the I···H/D–C hydrogen/deuterium bonding and other noncovalent interactions (viz. tetrel-, pnictogen- and lump-hole bonding interactions) that are ubiquitous in the orthorhombic CH3NH3PbI3/CD3ND3PbI3 perovskite geometry. Their interplay determines the overall geometry of the polymorph, and are therefore responsible in part for the emergence of the functional optical properties of this material. This study also suggests that these interactions should not be regarded as the sole determinants of octahedral tilting since lattice dynamics is known to play a critical role as well, a common feature in many inorganic perovskites both in the presence and the absence of the encaged cation, as in CsPbI3/WO3 perovskites, for example.

Investigation of intramolecular hydrogen bonding in conjunction with cation-π interactions in complexes involving 4-substituted-8-hydroxyquinolines

Intramolecular hydrogen bonding interactions together with non-covalent cation-π interactions of the Na+ cation in 4-substituted-8-hydroxyquinolines were investigated using quantum mechanical calculations to know results of reciprocal effects of these interactions. Also, cation-π interactions of Na+ cation on 4-substituted-quinolines as a similar system without intramolecular hydrogen bonding were considered to compare binary complexes Na+-X-8-hydroxyquinolines and Na+-X-quinolines (where X is used as a replacement for 4-substituted and X = OH, CH3, H, F, Cl, CF3, and CN). Geometrical parameters, Hammett constants, and electronic properties were studied to interpret the binding energies. A new formulation was proposed to compute energy of intramolecular hydrogen bonding interactions based on atoms in molecules (AIM) analysis and properties of electron charge densities at ring critical points (RCPs). Also, population analysis was performed using natural bond orbital (NBO) method to find role of donor-acceptor interactions on stability of the complexes. Indeed, localized molecular orbital energy decomposition analysis (LMO-EDA) was employed to realize contribution of components of energy in stability of the complexes.

Structural, optical and charge density analysis of Al doped ZnO Materials

The hexagonal structured Zn1−xAlxO (x = 0.00, 0.04, 0.06, 0.08 and 0.10) materials was synthesized by co-precipitation method. Structural, morphological and photoluminescence properties of Al doped ZnO powders were investigated by powder X-ray diffraction, scanning electron microscopy and photoluminescence characterizations, respectively. Structural analysis was done by Rietveld refinement technique. The spherical shaped morphology was observed in ZnO:Al powders. The bonding features were analyzed by using electron density distribution studies and the photoluminescence properties of Zn1−xAlxO (x = 0.00, 0.04, 0.06, 0.08 and 0.10) was also revealed.

Ab Initio Study of the Interface of the Solid-State Electrolyte Li9N2Cl3 with a Li-Metal Electrode

Ab initio molecular dynamics study of an electrochemical interface between a solid-state-electrolyte Li9N2Cl3 and a Li-metal is performed to analyze interphase formation due to electrochemical instability. An external electric field is applied to emulate the interface under charging conditions. At open circuit, we observed electrochemical stability at both sides of the interface, without electrolyte decomposition, or new phase formation, in good agreement with reported experiments. However, a structural re-accommodation takes place at both sides of the interface. Some oxidation of the surface Li-atoms takes place when Cl and N anions capture Li from the metal to complete octahedral structures, a Bader charge and electron density analyses explain the difference between Cl and N behavior. At the interface with the Li9N2Cl3 (002) facet, the larger negative charge on low-coordinated N atoms is able to retain more Li atoms than the Cl atoms do. At charging conditions applying an external electric field (0.5 V/Å), no major changes are observed in atomic diffusion or structural changes at the interphase; however, the main difference is the change of the Li-metal crystal structure. Due to migration of Li from the metal anode to the electrolyte, vacancies are created on the anode, causing a structural re-arrangement at the anode surface.

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.

Physical properties of ThCr2Si2-type Rh-based compounds ARh2Ge2(A = Ca, Sr, Y and Ba): DFT based first-principles investigation

In this paper, we have explored the physical, mechanical, chemical bonding, dialectical and thermodynamic properties of ARh2Ge2 (A = Ca, Sr, Y and Ba) theoretically for the first time. This investigation has been completed by density functional theory (DFT) calculations with the help of CASTEP code. The structural optimized factors of ARh2Ge2 (A = Ca, Sr, Y and Ba) are in excellent concurrence with the existing experimental data. The observed elastic constants are positive and prove the mechanical constancy for all these compounds. The calculated Pugh’s ratio and Poisson’s ratio show the ductile behaviors of Ca/YRh2Ge2 and brittleness behaviors of Sr/BaRh2Ge2, whereas the Cauchy pressure indicates the ductility for all these phases. The anisotropic factors, universal anisotropy indicator and fraction of anisotropy in compression and shear ensure the elastically anisotropic nature for all these phases. Bulk modulus and hardness values indicate that Sr/BaRh2Ge2 are soft and easily machinable in comparison with Y/CaRh2Ge2. The analysis of the band structure diagrams as well as density of states (total density of states and partial density of states) evidence the metallic behavior for all the compounds. The analysis of Mulliken bond populations and charge density maps give the existence of covalent and metallic bonding in these compounds. The optical properties point out that all phases can be used as coating materials at low energies. For all the phases the Debye temperatures have been calculated via elastic constant data. We have also evaluated the minimum thermal conductivity for these compounds. All compounds possess the relatively low minimum thermal conductivity with the low value of Debye temperatures which also evidence that all compounds could be applied like thermal fence covering material.

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.

First-principles investigation of the electronic band structures and optical properties of quaternary ABaMQ4 (A = Rb, Cs; M = P, V; and Q = S) metal chalcogenides

In this paper, we study the optoelectronic properties of quaternary metal chalcogenide semiconductor ABaMQ4 (A = Rb, Cs; M = P, V; and Q = S) compounds using state-of-the-art density functional theory (DFT) with TB-mBJ approximation for the treatment of exchange-correlation energy. In particular, the electronic and optical properties of the relaxed geometries of these compounds are investigated. Our first-principles ab-initio calculations show that the CsBaPS4 and RbBaPS4 compounds have direct bandgaps whereas the CsBaVS4 compound exhibits indirect bandgap nature. Importantly, the theoretically calculated values of the bandgaps of the compounds are consistent with experiment. Furthermore, our analysis of the electronic charge densities of these compounds indicates that the above quaternary chalcogenides have mixed covalent and ionic bonding characters. The effective masses of these compounds are also calculated which provide very useful information about the band structure and transport characteristics of the investigated compounds. Similarly, high absorptivity in the visible and ultraviolet regions of the electromagnetic spectrum possibly predicts and indicates the importance of these materials for potential optoelectronic applications in this range.

Topology of electron density and electrostatic potential of HIV reverse transcriptase inhibitor zidovudine from high resolution X-ray diffraction and charge density analysis

Azidothymidine (AZT) is a first anti-HIV drug namely Zidovudine used for HIV treatment, which binds to the viral DNA primer and inhibits the HIV reverse transcription. The side effects of this powerful drug are severe and the detailed understanding of its electronic structure helps to design new drugs from the AZT molecule. Present study aims to determine the structure of AZT at electronic level from the experimental charge density analysis as well as the solid state DFT calculations. AZT was crystallized and low temperature high resolution X-ray diffraction intensity data has been measured up to sin (θ/λ)max = 1.1 Å−1 at 100.0 (2) K. The crystal structure of AZT was determined, which reveals the information that the AZT compound crystallizes with two molecules in the asymmetric unit which are conformationally different and linked through strong hydrogen bonding interactions (dimer). The Hirshfeld surface of both molecules shows the locations of weak and strong interactions. Further, a multipole model refinement was carried out using Hansen-Coppens multipole formalism. The experimental topological properties of electron density of AZT molecules were determined and compared with the results of theoretical DFT calculations based on solid state and gas phase studies. The charge density distribution of the two molecules in the asymmetric unit is unequal and shows some difference. The topological properties of O–H⋅⋅⋅O, O–H⋅⋅⋅N, C–H⋅⋅⋅N, H⋅⋅⋅H and azide⋅⋅⋅azide group interactions are also determined. The electrostatic potential (ESP) surface of both AZT molecules in the crystal exhibits high electronegative regions around the O, N atoms and also around the azide group, however, ESP regions of molecules (I) and (II) are not similar.

Evaluation of electronic state of Cs-adsorbed clay minerals by NEXAFS analysis using DFT calculations

A combined analytical method of NEXAFS measurement and DFT-calculation was employed for the evaluation of Cs states in clay minerals. The measured Cs M4,5 NEXAFS spectra of Cs halides were analyzed using the DFT-calculations in order to establish the analytical methods. The NEXAFS spectra of the Cs halides were well reproduced by incorporating the core-hole strength. The Cs M4,5 NEXAFS spectrum of the clay minerals was well reproduced by the DFT-calculations including the major transitions and tail structures with the established method. Further evaluation of this spectrum by charge density analysis suggested that these major transitions and the tail structures likely reflect the bonding state and the local environment around the Cs atoms. Comparison of electronic states of Cs in the clay mineral with those in the Cs halides by DFT-calculations has shown that the interaction between Cs and the nearest-neighbor atom is largest in the clay mineral, which differs from those of Cs halides. This happened due to the energy level of Cs-5s and 5p, which was closer to that of O-2s and 2p than the s and p orbitals of other alkali metal and alkali earth metal elements.

The metal-free magnetism and ferromagnetic narrow gap semiconductor properties in graphene-like carbon nitride

In spintronics, if a two-dimensional (2D) organic metal-free material has stable magnetism and narrow gap semiconductor properties, it will have a very bright application prospect. A graphene-like carbon nitride (g-C13N13) that we design just meets these requirements. As a new structure, firstly the stability of the g-C13N13 has been verified. It has stable electron spin polarization and the magnetic moment of each primitive cell is 1μB. It exhibits ferromagnetic narrow gap semiconductor properties through our analysis of energy band structure and charge density. Ferromagnetic ordering between two adjacent primitive cells is stable. The Monte Carlo simulation using the Ising model shows the Curie temperature material is 204 K. Our research is an inspiration for the applications of this kind of materials in spintronics devices.

Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis

Alzheimer disease (AD) is a cruel neurodegenerative disorder caused by the deposition of amyloid β (Aβ) peptide inside the brain. The β-secretase (beta amyloid precursor protein (APP) cleaving enzyme 1, BACE1) is one of the enzymes involved in the cleavage of APP that leads to the Aβ formation and it is the primary target for the treatment of AD. Recent report outlines that verubecestat molecule strongly inhibits BACE1; however, its structure, binding mechanism and the stability in the active site of BACE1 are not yet known. The present study aims to determine the structure, binding affinity and the stability of verubecestat molecule in the active site of BACE1 from the molecular docking, quantum mechanics/molecular mechanics (QM/MM)-based charge density analysis and molecular dynamics simulation. Verubecestat molecule was docked at BACE1; it shows high binding affinity towards BACE1. Further, the conformational geometry and the intermolecular interactions of verubecestat in the active site of BACE1 were determined. The molecule forms strong interaction with the neighboring amino acids in the active site of BACE1. The onsite QM/MM-based charge density analysis reveals the nature of charge density distribution and the topological properties of intermolecular interactions of verubecestat molecule in the active site of BACE1. The calculated electrostatic potential (ESP) of verubecestat in the active site of BACE1 displays high negative and positive ESP regions of the molecule. This onsite QM/MM analysis is more relevant to the physiological situation. The molecular dynamics simulation has been performed, which confirms the high stability and compactness of verubecestat in the active site of BACE1. The MM-generalized Born surface area and MM-Poisson Boltzmann surface area free energy calculations of verubecestat–BACE1 also confirm the high binding affinity of verubecestat.Communicated by Ramaswamy H. Sarma

Excitation Energies of Localized Correlated Defects via Quantum Monte Carlo: A Case Study of Mn4+-Doped Phosphors

Accurate excitation energies of localized defects have been a long-standing problem for electronic structure calculation methods. Using Mn4+-doped solids as our proof of principle, we show that diffusion quantum Monte Carlo (DMC) is able to predict phosphorescence emission energies within statistical error. To demonstrate the generality of our DMC approach for other possible localized defects, we conduct charge density analyses using DMC and density functional theory (DFT). We also identify a new material with an emission energy of 1.97(8) eV, which is close to the optimum of 2.03 eV for a red-emitting phosphor. To our knowledge, our work is the first report on studying excitation energies of a transition metal impurity using an ab initio many-body electronic structure method. In contrast, semilocal and hybrid-DFT largely underestimates, and fails to reproduce, some of the trends in the emission energies. Our work underscores the importance of an accurate account of exchange, correlation, and excitonic effects for localized excitations in defective solids.

Design and analysis of electric potential and space charge density in a portable electrostatic precipitator

This paper presents the analysis of electric potential and space charge density distribution for different high DC voltage between discharge electrodes and collecting plates in a Portable Needle-Plate electrostatic precipitator.

First-Principles Determination of Active Sites of Ni Metal-Based Electrocatalysts for Hydrogen Evolution Reaction.

The determination of active sites of materials is essential for the molecular design of high-performance catalysts. In this study, the first-principles method is applied to investigate the active sites of low-cost Ni metal-based electrocatalysts for hydrogen evolution reactions (HER), which is a promising alternative to expensive Pt metal-based catalysts. The adsorption of hydrogen on different sites of pristine and partially oxidized Ni(111) surface is investigated. All of the possible configurations have been systematically investigated here with the consideration of their Boltzmann distribution. Using the Gibbs free energy of intermediate H atoms (Δ GH*) as a descriptor, it is found that the Δ GH* increases with the increase of the coverage of oxygen atoms. The slightly oxidized surface Ni atoms are theoretically identified to be the best catalytic centers for the electrocatalytic HERs when the coverage of oxygen is considerably low. On the basis of the analyses of Bader charge distribution and density of states, our results reveal that the superior performance of the slightly oxidized surface Ni atoms can be ascribed to the optimal electronic properties.

Built-in electric field-assisted charge separation over carbon dots-modified Bi2WO6 nanoplates for photodegradation

Bi2WO6 photocatalyst has attracted much interest but suffers from easy recombination of electron-hole pairs. Herein carbon dots (CDs) as a cocatalyst were hydrothermally hybridized with Bi2WO6 nanoplates with aim of efficient separation of charge carriers. Electron transfer from CDs to Bi2WO6 across their interfaces upon contact was revealed by XPS results and further supported by differential charge density analyses. Such electron transfer led to a built-in electric field pointing from CDs to Bi2WO6, which drove photoinduced electrons flowing to CDs under light irradiation. DFT simulation showed the introduced electron was mainly distributed on CDs instead of Bi2WO6, which implied that CDs had impressive capability of taking photoinduced electrons under irradiation. Such efficient charge separation was experimentally supported by photoelectrochemical analyses. The superoxide radicals and holes were found to participate in the photodegradation of RhB under visible light irradiation. The enhanced photocatalytic activity of CDs/Bi2WO6 could be ascribed to the efficient charge separation and large specific area of Bi2WO6 nanoplates.

Charge density analysis attending bond torsion: A bond bundle case study

AbstractFor nearly a century chemical understanding has been tied to the properties of bonds, although more often than not, these bond properties are rooted in molecular orbital or valence bond representations of the electronic structure. Technological advances, however, are allowing for experimental measurements of the density via high resolution X‐ray diffraction, while theoretical insights are opening the door to its direct calculation using fast and potentially versatile orbital free DFT methods. Capitalizing on these emerging tools without sacrificing orbital derived understanding has spurred a search for density based representations that deliver the same information available from the orbital perspective. We show that recent extensions of the QTAIM formalism are useful as a means of recovering some of the bond properties that have become an intrinsic part of our chemical understanding. Specifically, we compute from the density the changing bond order and bond order distribution accompanying the rotation about a double bond using the well‐studied fulvene molecule as a test case. We compare the picture that emerges from this density based perspective with that stemming from molecular orbital approaches and argue that the two viewpoints are compatible.