On point perforating defects in bilayer structures

This article deals with the issue of perforating point defects (pores) in a bilayer heterostructure composed of striped borophene and graphene. Three types of non-equivalent vacancies of the minimum size are considered. These include a single vacancy and two double vacancies. The study of the properties and stability of the perforating defects in borophene-graphene heterostructures is important given the increasing role of such structures in membranes for water purification, renewable energy generation, and other osmotic applications. Using the DFT method, the atomic configurations and main energy characteristics of the proposed defects are obtained. The results show that the formation of a single boron vacancy on the borophene side of borophene-graphene requires less energy than the formation of a carbon vacancy in graphene. Comparisons between double vacancies in nanoscale materials are unreliable because different reference systems produce the different chemical potentials. The problem of choosing the reference system for reliable calculation of the vacancy formation energies is posed and discussed. Using borophene-graphene as an example, it is shown that the reference system strongly affects the magnitude and sign of the vacancy formation energy. Hydrogenation is tested to stabilize the proposed defects.

Semiempirical Approach to the Fukui Function Analysis of Uric Acid under Different pH Conditions

Analytic Fukui functions calculated at a first-principles level are combined with experimental pKa values and the calculation of tautomerization energies to obtain the effective regioselectivity of uric acid toward electron-transfer reactions under different pH conditions. Second-order electron binding energies are also computed to determine which of the tautomers is more likely to participate in the electron transfer. A comparison of vertical and adiabatic proton detachment energies allows us to conclude that tautomerization is not mediating deprotonation and that two monoanionic species are of comparable relevance. The main difference between these monoanionic species is the ring that has been deprotonated. Both monoanionic species are produced from a single neutral tautomer and mainly produce a single dianionic tautomer. As a method for the analysis of systems affected by pH such as uric acid, we propose to plot condensed Fukui functions versus pH, allowing us to draw the effect of pH on the regioselectivity of electron transfer in a single image.

On the energetic and magnetic stability of neutral and charged lithium clusters doped with one and two yttrium atoms

DFT calculations were performed to study the effect on energetic and magnetic stability when clusters with up to 24 lithium atoms were doped with one and two atoms of yttrium. In this, the effect of the charge was considered. As a result, some stable structures were identified as possible magnetic superatoms, among them, the YLi₁₂⁺ cluster with an icosahedron geometry with a spin magnetic moment of 4 bohr magnetons. The participation of yttrium in the electron density of the unpaired electrons providing magnetism in clusters was corroborated at the level of a density of states (DOS) calculation and a spin density calculation. In particular, in the Y₂Li₁₂⁺ superatom, it was found that the encapsulated yttrium atom participates with 35.02% and the second yttrium atom with 15.04%. These percentages, with a contribution from p orbitals, but to a greater extent by d orbitals. The complementation to these percentages is due to the participation of the s and p orbitals of the lithium atoms. In general, doping with a second yttrium atom allowed to obtain a greater amount of high magnetic moments, and considering charged clusters allowed to obtain also high magnetic moments.

Fitting Multiplet Simulations to L-Edge XAS Spectra of Transition-Metal Complexes Using an Adaptive Grid Algorithm

A new methodology based on an adaptive grid algorithm followed by an analysis of the ground state from the fit parameters is presented to analyze and interpret experimental XAS L_2,3-edge data. The fitting method is tested first in a series of multiplet calculations for d⁰-d⁷ systems and for which the solution is known. In most cases, the algorithm is able to find the solution, except for a mixed-spin Co²⁺ O_h complex, where it instead revealed a correlation between the crystal field and the electron repulsion parameters near spin-crossover transition points. Furthermore, the results for the fitting of previously published experimental data sets on CaO, CaF₂, MnO, LiMnO₂, and Mn₂O₃ are presented and their solution discussed. The presented methodology has allowed the evaluation of the Jahn-Teller distortion in LiMnO₂, which is consistent with the observed implications in the development of batteries, which use this material. Moreover, a follow-up analysis of the ground state in Mn₂O₃ has demonstrated an unusual ground state for the highly distorted site which would be impossible to optimize in a perfect octahedral environment. Ultimately, the presented methodology can be used in the analysis of X-ray absorption spectroscopy data measured at the L_2,3-edge for a large number of materials and molecular complexes of first-row transition metals and can be expanded to the analysis of other X-ray spectroscopic data in future studies.

A Fukui Analysis of an Arginine-Modified Carbon Surface for the Electrochemical Sensing of Dopamine

Amino acid-modified carbon interfaces have huge applications in developing electrochemical sensing applications. Earlier reports suggested that the amine group of amino acids acted as an oxidation center at the amino acid-modified electrode interface. It was interesting to locate the oxidation centers of amino acids in the presence of guanidine. In the present work, we modeled the arginine-modified carbon interface and utilized frontier molecular orbitals and analytical Fukui functions based on the first principle study computations to analyze arginine-modified CPE (AMCPE) at a molecular level. The frontier molecular orbital and analytical Fukui results suggest that the guanidine (oxidation) and carboxylic acid (reduction) groups of arginine act as additional electron transfer sites on the AMCPE surface. To support the theoretical observations, we prepared the arginine-modified CPE (AMCPE) for the cyclic voltammetric sensing of dopamine (DA). The AMCPE showed excellent performance in detecting DA in blood serum samples.

Pre-post electron transfer regioselectivity at glycine modified graphene electrode interface for voltammetric sensing applications

In the last few years, glycine (GL) showed good experimental evidence as an electron transfer (ET) mediator at the carbon (in particular graphene (GR)) interface. However, ET properties of GL modified GR interface are still not known completely. These can be achieved using density functional theory-based models. Modelling of modified carbon electrode interfaces is essential in electroanalytical chemistry to get insights into their electronic and redox properties. Here we have modelled glycine modified graphene interface to find out its interfacial redox ET properties. Conceptual density functional theory concepts like frontier molecular orbital (FMO) theory and analytical Fukui functions were utilized to predict the ET sites on the modified graphene surface. It is shown that at the glycine-modified graphene interface, amine groups act as additional oxidation sites and carboxylic acid groups as additional reduction sites. Therefore, glycine acts as an ET mediator at the graphene-based electrode interface. The obtained results are well supported by previously published experimental reports.

Studies of Monoamine Neurotransmitters at Nanomolar Levels Using Carbon Material Electrodes: A Review

Neurotransmitters (NTs) with hydroxyl groups can now be identified electrochemically, utilizing a variety of electrodes and voltammetric techniques. In particular, in monoamine, the position of the hydroxyl groups might alter the sensing properties of a certain neurotransmitter. Numerous research studies using electrodes modified on their surfaces to better detect specific neurotransmitters when other interfering factors are present are reviewed to improve the precision of these measures. An investigation of the monoamine neurotransmitters at nanoscale using electrochemical methods is the primary goal of this review article. It will be used to determine which sort of electrode is ideal for this purpose. The use of carbon materials, such as graphite carbon fiber, carbon fiber micro-electrodes, glassy carbon, and 3D printed electrodes are only some of the electrodes with surface modifications that can be utilized for this purpose. Electrochemical methods for real-time detection and quantification of monoamine neurotransmitters in real samples at the nanomolar level are summarized in this paper.

Electronic structure and reactivity indexes of cobalt clusters, both pure and mixed with NO and [Formula: see text] ([Formula: see text], [Formula: see text] and [Formula: see text])

Among the most popular motivations for environmental scientists is improving materials that could be useful to fight or avoid pollution. This work shows a study of neutral and cationic cobalt clusters from 4 to 9 atoms ([Formula: see text], q = 0,1 and n = 4-9) to model their separate interaction with contaminant nitric and nitrous oxides. This study is within the framework of the density functional theory in the Kohn-Sham scheme by using BPW91 functional and 6-311G and 6-31G* basis sets to calculate global and local reactivity indexes. The effect of spin multiplicity is also determined. Results on the geometries of pure cobalt clusters agree with previously reported structures. Global minimum energy structures showed a marked preference towards the interaction of nitric and nitrous oxide molecules with cobalt clusters through chemisorptive dissociation, with the dissociation of the corresponding nitrogen oxide. Reactivity indexes reveal an even-odd alternate, which is related to electron counts. Moreover, the chemical potential is lowering after interaction with nitrogen oxides. The Fukui function illustrates the reactive zones with a high probability of chemisorption of more nitrogen oxide molecules.

Cis and trans platinum(II) N-heterocyclic carbene isomers: synthesis, characterization and biological activity

The synthesis of cis and trans geometrical isomers of platinum(II) complexes with a symmetric N-heterocyclic carbene ligand (MeNHC) is reported. These complexes were obtained from 1,3-dimethylimidazolium-2-carboxylate, a masked NHC precursor....

Analytic Alchemical Derivatives for the Analysis of Differential Acidity Assisted by the h Function

Analytical calculation of alchemical derivatives based on auxiliary density perturbation theory is described, coded, and validated. For the case where the nucleus is a hydrogen atom and the nuclear charge is changed from 1 to 0, it turns out that a good estimate of the proton binding energies can be obtained very efficiently. First-order results correspond exactly to the molecular electrostatic potential evaluated at the hydrogen nucleus location (removing self-repulsion), in agreement with previously reported extensive studies. Therefore, the second-order results reported here are refinements in accuracy that finally allow a quantitative exploration of differential acidity. Furthermore, the recently reported h function is produced in its analytical form as a byproduct and local descriptor associated with the proton binding energy values found with this approach. In an example application, proton binding energies are computed for a family of imidazolium derivatives to demonstrate the capabilities and the stability of the method with respect to changes in basis set or exchange-correlation functional.

Asymmetric Density Fitting with Modified Cholesky Decomposition Applied to Second-Order Electron Propagator

Computation of molecular orbital electron repulsion integrals (MO-ERIs) as a transformation from atomic orbital ERIs (AO-ERIs) is the bottleneck of second-order electron propagator calculations when a single orbital is studied. In this contribution, asymmetric density fitting is combined with modified Cholesky decomposition to generate efficiently the required MO-ERIs. The key point of the presented algorithms is to keep track of integrals through partial contractions performed on three-center AO-ERIs; these contractions are stored in RAM instead of the AO-ERIs. Two implementations are provided, an in-core, which reduces the arithmetic and memory scaling factors as compared to the four-center AO-ERIs contraction method, and a semidirect, which overcomes memory limitations by evaluating antisymmetrized MO-ERIs in batches. On the numerical side, the proposed approach is fast and stable. The bad effects due to ill conditioning, namely, several negative and close to zero eigenvalues due to machine round off errors of the matrix associated with the density fitting process, are effectively controlled by means of a modified Cholesky factorization that avoids the matrix inversion needed to perform the asymmetrical density fitting implementation. The numerical experience presented shows that the in-core implementation is highly competitive to perform calculations on medium and large basis sets, while the semidirect implementation has small variations in time by changes in the available memory. The general applicability is illustrated on a set of selected relatively large-size molecules.

Exploring the Structure, Energetic, and Magnetic Properties of Neutral Small Lithium Clusters Doped with Yttrium: Supermagnetic Atom Research

Density functional theory calculations based on magnetic and energetic stability criteria were performed to study a series of yttrium-doped lithium neutral clusters. A relativistic approximation was employed to properly describe the energy and multiplicity of the given clusters' fundamental states. The interaction of the 4d-Y atomic orbitals with the sp-Li states had an important role in the magnetic and energetic behavior of the selected systems. The spin density was concentrated over the yttrium atom regardless of the size of the cluster. Li7Y is a new stable superatom due to its enhanced magnetic properties.

Quantum chemical and electrochemical studies of lysine modified carbon paste electrode surfaces for sensing dopamine

We have improved the sensitivity of a carbon paste electrode from lysine for the sensitive detection of dopamine.

Regioselectivity in hexagonal boron nitride co-doped graphene

The active electron transfer (ET) sites on the graphene surface can be controlled by hexagonal boron nitride (h-BN) doping.

Auxiliary Density Perturbation Theory for Restricted Open-Shell Systems

The recently developed approach to auxiliary density perturbation theory (<em>J. Chem. Phys.</em> <strong>2008</strong>, <em>128</em>, 134105) for the purpose of calculating molecular properties is here extended to include open-shell systems. Both unrestricted and restricted formalisms are considered. A linear equation system, twice as large as the auxiliary function set is obtained in both cases. For the first time, the formulation for auxiliary density perturbation theory for restricted open-shell formalism is derived.

Initial stage of the degradation of three common neonicotinoids: theoretical prediction of charge transfer sites

Tautomerization of acetamiprid gives alternatives to search new pathways for its degradation in water.

Extended source model for diffusive coupling

Motivated by the prevailing approach to diffusion coupling phenomena which considers point-like diffusing sources, we derived an analogous expression for the concentration rate of change of diffusively coupled extended containers. The proposed equation, together with expressions based on solutions to the diffusion equation, is intended to be applied to the numerical solution of systems exclusively composed of ordinary differential equations, however is able to account for effects due the finite size of the coupled sources.

Half-numerical evaluation of pseudopotential integrals

A half-numeric algorithm for the evaluation of effective core potential integrals over Cartesian Gaussian functions is described. Local and semilocal integrals are separated into two-dimensional angular and one-dimensional radial integrals. The angular integrals are evaluated analytically using a general approach that has no limitation for the l-quantum number. The radial integrals are calculated by an adaptive one-dimensional numerical quadrature. For the semilocal radial part a pretabulation scheme is used. This pretabulation simplifies the handling of radial integrals, makes their calculation much faster, and allows their easy reuse for different integrals within a given shell combination. The implementation of this new algorithm is described and its performance is analyzed.

Structures and vibrations of Nb3O and Nb3O−: A density functional study

Density functional calculations of neutral and anionic niobium trimer monoxides are presented. The calculations were performed employing scalar quasirelativistic effective core potentials. In order to test the accuracy of the used effective core potentials in the framework of density functional theory the pulsed field ionization-zero electron kinetic energy photoelectron spectrum of Nb(3)O was simulated and compared to experiment. Different isomers of Nb(3)O and Nb(3)O(-) were studied in order to determine the ground state structures. For both neutral and anionic systems a planar C(2v) structure with an edge-bound oxygen atom was found as a ground state. Equilibrium structure parameters, harmonic frequencies, and adiabatic electron affinity are reported. The calculated electron affinity and frequencies are in good agreement with the available experimental data obtained recently from vibrationally resolved negative ion photoelectron spectroscopy.

Efficient and reliable numerical integration of exchange-correlation energies and potentials

An adaptive numerical integrator for the exchange-correlation energy and potential is presented. It uses the diagonal elements of the exchange-correlation potential matrix as a grid generating function. The only input parameter is the requested grid tolerance. In combination with a defined cell function the adaptive grid generation scales almost linear with the number of basis functions in a system. With the adaptive numerical integrator the self-consistent field energy error, which is due to the numerical integration of the exchange-correlation energy, converges with increasing adaptive grid size to a reference value. The performance of the adaptive numerical integration is analyzed using molecules with first, second, and third row elements. Especially for transition metal systems the adaptive numerical integrator shows considerably improved performance and reliability.