Relativistic Density Functional Theory Calculations Research Articles

Periodic Bonding Behaviors of Actinide Atoms (An = Th-Cm) with Negatively Curved Nanographene.

The nanographene with negative curvature has been extensively studied due to its interesting properties and potential applications. In the present work, we have performed all-electron scalar relativistic density functional theory (DFT) calculations to understand the periodic interaction mechanisms of actinide atoms (An = Th, Cm) with the TB8C nanographene. The encapsulated complexes (An@TB8C) were formed due to the octagonal vacancy in the TB8C nanographene. TB8C shows fairly high affinity toward An atoms, especially for Th and Pa. AIMD simulations further confirmed the effective trapping of An atom with TB8C. The partial covalent characters of An-C bonds in An@TB8C were revealed through various bond analysis methods. The 6d electrons of An play an important role in the participation of chemical bonds. The delocalization index (DI) is proposed as a useful descriptor in the study of bond strength involving the actinides. Electronic absorption spectra were simulated for further identification in the experiments. The current work has expanded the potential molecular properties and applications of nanographene.

A pH switchable hydrophilic fluorescent BODIPY sodium disulfonate for Fe3+ multicolor detection: Experimental and DFT studies

BODIPY-based chemosensors are widely used owing to merits like good selectivity, high fluorescence quantum yield, and excellent optical stability. As such, a pH-switchable hydrophilic fluorescent probe, BODIPY-PY-(SO3Na)2, was developed for detection of Fe3+ ion in aqueous solutions. BODIPY-PY-(SO3Na)2 revealed strong fluorescence intensity and was responsive to pH value in the range of 6.59–1.96. Additionally, BODIPY-PY-(SO3Na)2 showed good selectivity and sensitivity towards Fe3+. A good linear relationship for Fe3+ detection was obtained from 0.0 μM to 50.0 μM with low detecting limit of 6.34 nM at pH 6.59 and 2.36 nM at pH 4.32, respectively. The response to pH and detection of Fe3+ induced obvious multicolor changes. BODIPY-PY-(SO3Na)2 can also be utilized to quantitatively detect Fe3+ in real water sample. Different mechanisms of Fe3+ detection at investigated pH values were unraveled through relativistic density functional theory (DFT) calculations in BODIPY-PY-(SO3Na)2 and experiments of coexisting cations, anions and molecules. These results enabled us to gain a deeper understanding of the interactions between BODIPY-PY-(SO3Na)2 and Fe3+ and provide valuable fundamental information for design of efficient multicolor chemosensors for Fe3+ as well.

Reactivity of Zinc Fingers in Oxidizing Environments: Insight from Molecular Models Through Activation Strain Analysis.

The reactivity of Zn2+ tetrahedral complexes with H2O2 was investigated in silico, as a first step in their disruption process. The substrates were chosen to represent the cores of three different zinc finger protein motifs, i. e., a Zn2+ ion coordinated to four cysteines (CCCC), to three cysteines and one histidine (CCCH), and to two cysteines and two histidines (CCHH). The cysteine and histidine ligands were further simplified to methyl thiolate and imidazole, respectively. H2O2 was chosen as an oxidizing agent due to its biological role as a metabolic product and species involved in signaling processes. The mechanism of oxidation of a coordinated cysteinate to sulfenate-κS and the trends for the different substrates were rationalized through activation strain analysis and energy decomposition analysis in the framework of scalar relativistic Density Functional Theory (DFT) calculations at ZORA-M06/TZ2P ae // ZORA-BLYP-D3(BJ)/TZ2P. CCCC is oxidized most easily, an outcome explained considering both electrostatic and orbital interactions. The isomerization to sulfenate-κO was attempted to assess whether this step may affect the ligand dissociation; however, it was found to introduce a kinetic barrier without improving the energetics of the dissociation. Lastly, ligand exchange with free thiolates and selenolates was investigated as a trigger for ligand dissociation, possibly leading to metal ejection; molecular docking simulations also support this hypothesis.

Complexation of trivalent Eu and Am ions with phenanthroline-derived ligands tuned by rotating thiazole/oxazole substituents

The reprocessing of spent nuclear fuels is greatly challenging, as the current separation technique of lanthanide (Ln) and actinide (An) suffers too many difficulties. In this paper, selective ligands of phenanthroline derivatives modified by thiazole/oxazole were designed by relativistic density functional theory calculations. Their complexation of Eu3+ and Am3+ and the mechanism of selective separation were comprehensively examined. The spatial rotation against the CC bond between phenanthroline and thiazole/oxazole has access to six ligands. It is shown that Looo with oxazole substituents and their oxygens being opposite is the best electron donor for metal ions. The results of WBIs and MBO unravel that Am-L bond has more covalency than respective Eu-L bond. From topological analyses, it is found that these metal–ligand bonds are dominated by electrostatic interaction and largely of ionic bond character. Thermodynamically, all ligands prefer binding Eu3+ to Am3+.

Bis(acyl)phosphide Complexes of U(III)/U(IV): A Case of a Hidden Redox-Active Ligand.

The recently reported tris(bis(2,4,6-triisopropylbenzoyl)-phosphide)uranium (UIII(trippBAP)3, 2) complex (Inorg. Chem. 2022, 61 (32), 12508-12517) demonstrated a silent 31P NMR spectrum. This complex was described as a U(III) complex with an organic radical ligand fragment. Moreover, the EPR spectrum of 2 was indicative of an organic radical in the ligand framework complexed to uranium, in contrast to that of UIV(mesBAP)4, 1. Herein, with the help of relativistic density functional theory (DFT) calculations, the electronic structures of 1, 2, and U(mesBAP)3 (4) are examined in an effort to understand the unusual 31P NMR spectrum of 2. Results indicate the reduction of the carbonyl bonds and delocalization of the electrons over the ligands, indicative of U → L backbonding. Additionally, the reduced acyl carbons are found to exist as ketyl radicals [O═C• -] that are responsible for the silent 31P NMR spectra of 2. These findings demonstrate the redox noninnocent nature of BAP- in 2 and 4, causing uranium to exist in a formal oxidation state of +4.

Reactivity of Ts and At oxides and oxyhydrides with a gold surface from periodic DFT calculations.

Adsorption energies, Eads, of oxides and oxyhydrides of the superheavy element (SHEs) Ts and of its lighter homologue At on the gold surface are predicted on the basis of relativistic periodic density functional theory calculations via AMS BAND software. The following compounds were considered: MO, MO2, MOO, and MO(OH) (where M = At and Ts). The aim of this study is to support "one-atom-at-a-time" gas-phase chromatography experiments on reactivity/volatility of SHEs. The results obtained indicate that all the molecules investigated should interact fairly strongly with the gold surface, with those of Ts being more reactive than At ones. The similarity in the Eads values of all the considered At compounds would make it challenging to differentiate between them while measuring their adsorption enthalpies, given experimental uncertainty. However, the difference in Eads among Ts compounds is more pronounced, so that one should be able to differentiate between the species.

Relativistic DFT Calculations of Cadmium and Selenium Solid-State NMR Spectra of CdSe Nanocrystal Surfaces.

Solid-state NMR spectra have been used to probe the structure of CdSe nanocrystals and propose detailed models of their surface structures. Density functional theory (DFT)-optimized cluster models that represent probable molecular structures of carboxylate-coordinated surface sites have been proposed. However, to the best of our knowledge, 113Cd and 77Se chemical shifts have not been calculated for these surface models. We performed relativistic DFT calculations of cadmium and selenium magnetic shielding tensors on model compounds with previously measured solid-state NMR spectra with (i) the four-component Dirac-Kohn-Sham (DKS) Hamiltonian and (ii) the scalar and (iii) spin-orbit levels within the ZORA Hamiltonian. Molecular clusters with Cd and Se sites in varying bonding environments were used to model CdSe (100) and CdSe(111) surfaces capped with carboxylic acid ligands. Our calculations identify the observed 113Cd isotropic chemical shifts δ(iso) of -465, -318, and -146 ppm arising from CdSeO3, CdSe2O2, and CdSe3O surface groups, respectively, with very good agreement with experimental measurements. The 113Cd chemical shifts linearly decrease with the number of O-neighbors. The calculated spans (δ11 - δ33) encompass the experimental values for CdSe3O and CdSe2O2 clusters but are slightly larger than the measured value for CdSeO3 clusters. Relativistic DFT calculations predicted a one-bond 113Cd-77Se scalar coupling of 258 Hz, which is in good agreement with the experimental values of 250 Hz. With a dense coverage of carboxylic acid ligands, the CdSe (100) surface shows a distribution of Cd-Se bond lengths and J-couplings. Relativistic DFT simulations thus aid in interpretation of NMR spectra of CdSe nanocrystals and related nanomaterials.

Novel Computational Chemistry Infrastructure for Simulating Astatide in Water: From Basis Sets to Force Fields Using Particle Swarm Optimization.

Using the example of astatine, the heaviest naturally occurring halogen whose isotope At-211 has promising medical applications, we propose a new infrastructure for large-scale computational models of heavy elements with strong relativistic effects. In particular, we focus on developing an accurate force field for At- in water based on reliable relativistic density functional theory (DFT) calculations. To ensure the reliability of such calculations, we design novel basis sets for relativistic DFT, via the particle swarm optimization algorithm to optimize the coefficients of the new basis sets and the polarization-consistent basis set idea's extension to heavy elements to eliminate the basis set error from DFT calculations. The resulting basis sets enable the well-grounded evaluation of relativistic DFT against "gold-standard" CCSD(T) results. Accounting for strong relativistic effects, including spin-orbit interaction, via our redesigned infrastructure, we elucidate a noticeable dissimilarity between At- and I- in halide-water force field parameters, radial distribution functions, diffusion coefficients, and hydration energies. This work establishes the framework for the systematic development of polarization-consistent basis sets for relativistic DFT and accurate force fields for molecular dynamics simulations to be used in large-scale models of complex molecular systems with elements from the bottom of the periodic table, including actinides and even superheavy elements.

Influence of the ligand-field on EPR parameters of cis- and trans-isomers in MoV systems relevant to molybdenum enzymes: Experimental and density functional theory study

The electron paramagnetic resonance (EPR) investigation of mononuclear cis- and trans-(L1O)MoOCl2 complexes [L1OH = bis(3,5-dimethylpyrazolyl)-3-tert-butyl-2-hydroxy-5-methylphenyl)methane] reveals a significant difference in their spin Hamiltonian parameters which reflect different equatorial and axial ligand fields created by the heteroscorpionate donor atoms. Density functional theory (DFT) was used to calculate the values of principal components and relative orientations of the g and A tensors, and the molecular framework in four pairs of isomeric mononuclear oxo‑molybdenum(V) complexes (cis- and trans-(L1O)MoOCl2, cis,cis- and cis,trans-(L-N2S2)MoOCl [L-N2S2H2 = N,N′-dimethyl-N,N′-bis(mercaptophenyl)ethylenediamine], cis,cis- and cis,trans-(L-N2S2)MoO(SCN), and cis- and trans-[(dt)2MoO(OMe)]2− [dtH2 = 2,3-dimercapto-2-butene]). Scalar relativistic DFT calculations were conducted using three different exchange-correlation functionals. It was found that the use of hybrid exchange-correlation functional with 25% of the Hartree-Fock exchange leads to the best quantitative agreement between theory and experiment. A simplified ligand-field approach was used to analyze the influence of the ligand fields in all cis- and trans-isomers on energies and contributions of molybdenum d-orbital manifold to g and A tensors and relative orientations. Specifically, contributions that originated from the spin-orbit coupling of the dxz, dyz, and dx2-y2 orbitals into the ground state have been discussed. The new findings are discussed in the context of the experimental data of mononuclear molybdoenzyme, DMSO reductase.

Front Cover: Fully Tin‐Coated Coinage Metal Ions: A Pincer‐Type Bis‐stannylene Ligand for Exclusive Tetrahedral Complexation (Chem. Eur. J. 27/2023)

A novel bis-stannylene pincer-type ligand has been prepared for the exclusive tetrahedral coordination of coinage metals. All compounds feature photoluminescent properties in the solid state. Detailed investigations by all-electron relativistic density functional theory calculations were performed. More information can be found in the Research Article by P. W. Roesky and co-workers (DOI: 10.1002/chem.202203583). Cover artwork by Alicia Schmidt.

New insights into the reactivity of the triscyclopentadienyl monothiolate uranium(IV) complexes: CS2 and CO2 insertion and redox properties. A DFT theoretical approach

The structural properties of a series of triscyclopentadienyl monothiolate uranium(IV) complexes [U(Cp)3(SR)] (Cp = η5–C5H5; R = Me (1), iPr (2), Ph (3), tBu (4)) as well as their reactions with CO2 or CS2 leading to their insertion into the US bond, have been investigated using relativistic Density Functional Theory (DFT) calculations. The computed activation barriers of these reactions show that insertion of CO2 into the US bond of the thiolate complexes is easier and faster than that of CS2, in agreement with the experimental observation. The study brings to light the electrostatic interactions and steric hindrance effects that play an important role in these processes. The redox behavior of the thiolate [U(Cp)3(SR)] complexes has also been investigated, permitting to find a very nice linear correlation (R2 = 0.99) between the computed electron affinities and the experimental reduction half–wave potentials E1/2. This correlation allowed to estimate the reduction potentials of [U(Cp)3(SMe)] (1) and [U(Cp)3(StBu)] (4) for which the electrochemical measurement failed. Several population analyses were carried out, among them Nalewajski–Mrozek Bond Orders (NMBO) and Hirshfeld charges Analysis (HA) allowing to rationalize the insertion reactions and redox processes and to highlight the driving role of the uranium 5f orbitals.

Fully Tin-Coated Coinage Metal Ions: A Pincer-Type Bis-stannylene Ligand for Exclusive Tetrahedral Complexation.

The synthesis of a novel bis-stannylene pincer ligand and its complexation with coinage metals (CuI , AgI and AuI ) are described. All coinage metal centres are in tetrahedral coordination environments in the solid state and are exclusively coordinated by four neutral SnII donors. 119 Sn NMR provided information about the behaviour in solution. All of the isolated compounds have photoluminescent properties, and these were investigated at low and elevated temperatures. Compared to the free bis-stannylene ligand, coordination to coinage metals led to an increase in the luminescence intensity. The new compounds were investigated in detail through all-electron relativistic density functional theory (DFT) calculations.

A theoretical study of the adsorption behavior of superheavy 7p-elements and their compounds on a surface of gold in comparison with their lighter homologs.

Adsorption energies, Eads, of the 7th row superheavy elements (SHEs) Lv through Og, as well as of the homologous species of the 6th row elements Po through Rn on a gold surface are predicted on the basis of relativistic periodic density functional theory calculations via SCM BAND software. Since some of the elements can also form compounds such as hydrides and oxyhydrides under experimental conditions, the Eads values of the MH (M = Bi/Mc, Po/Lv, At/Ts and Rn/Og) and MOH (M = At/Ts and Rn/Og) molecules on a gold surface were also calculated. The aim of this study is to support "one-atom-at-a-time" gas-phase chromatography experiments on the reactivity/volatility of SHEs. The obtained results show that, in agreement with earlier predictions using somewhat different approaches and with experimental results on Hg, Cn and Rn, the adsorption strength of the elements on the Au(111) surface should follow the sequence: Hg > Fl > Og > Cn ≫ Rn, with the Eads values of less than 100 kJ mol-1. The other elements and their compounds under consideration should adsorb much more strongly on the gold surface with Eads values above 160 kJ mol-1, which should make them indistinguishable with respect to Eads in the chromatography column kept at room temperature and lower. However, with the further detector development, investigations of the chemical properties of these short-lived and less volatile SHEs and their compounds at high temperatures should be possible.

Periodic trends in trivalent actinide halides, phosphates, and arsenates.

Due to the limited abundance of the actinide elements, computational methods, for now, remain an exclusive avenue to investigate the periodic trends across the actinide series. As every actinide element can exhibit a +3-oxidation state, we have explored model systems of gas-phase actinide trihalides, phosphates, and arsenates across the series to capture the periodic trends. By doing so, we were able to capture the periodic trends down the halogen series as well, and for the first time we are reporting a study on actinide astatides. Using scalar and spin-orbit relativistic Density Functional Theory (DFT) calculations, we have explored the variations in bond lengths, bond angles, and the charges on actinides (An). Despite the use of different sets of ligands, the trends remain similar. The properties of trivalent Pa, U, Np, and Pu are nearly identical; similar ionic radii could be the reason. The actinide elements show a tendency to exhibit a pre-Pu and a post-Cm behaviour, with Am acting as a switch. This could be due to the change in the behaviour from d-f-type to f-filling/d-type at around Pu-Cm in the actinides as already proposed in the previous literature. Bond lengths in the AnX3 increase down the halide series, and the atomic charges decrease on the actinide elements.

Superlattices of Gadolinium and Bismuth Based Thallium Dichalcogenides as Potential Magnetic Topological Insulators.

Using relativistic spin-polarized density functional theory calculations we investigate magnetism, electronic structure and topology of the ternary thallium gadolinium dichalcogenides TlGdZ2 (Z= Se and Te) as well as superlattices on their basis. We find TlGdZ2 to have an antiferromagnetic exchange coupling both within and between the Gd layers, which leads to frustration and a complex magnetic structure. The electronic structure calculations reveal both TlGdSe2 and TlGdTe2 to be topologically trivial semiconductors. However, as we show further, a three-dimensional (3D) magnetic topological insulator (TI) state can potentially be achieved by constructing superlattices of the TlGdZ2/(TlBiZ2)n type, in which structural units of TlGdZ2 are alternated with those of the isomorphic TlBiZ2 compounds, known to be non-magnetic 3D TIs. Our results suggest a new approach for achieving 3D magnetic TI phases in such superlattices which is applicable to a large family of thallium rare-earth dichalcogenides and is expected to yield a fertile and tunable playground for exotic topological physics.

BinPo: An open-source code to compute the band structure of two-dimensional electron systems

We introduce BinPo, an open-source Python code to compute electronic properties of two-dimensional electron systems. A bulk tight binding Hamiltonian is constructed from relativistic density functional theory calculations represented in the basis of maximally localized Wannier functions. BinPo has a Schrödinger-Poisson solver, integrating an electric field-dependent relative permittivity to obtain self-consistently the confining electrostatic potential energy term in the derived tight binding slab system. The band structure, energy slices, and other properties, along with different projections and orientations can be computed. High resolution and publishable figures of the simulations can be generated. In BinPo, priority has been given to ease-of-use, efficiency, readability and modularity, therefore becoming suitable to produce reliable electronic structures simulations at low computational cost. Along with the code itself, we provide files from first-principles calculations for some materials, instructions of use, and detailed examples of its wide range of capabilities. The code was developed with a focus on the ABO3 perovskite structure-based systems, such as SrTiO3 and KTaO3, because of their increasing impact in the materials community. Some features, such as the projection onto orbital states, are restricted to calculations using the relevant t2g orbitals for this family of materials, yet it is possible to include more elements in the basis for the band structure determination of other systems. The use of a relativistic approach allows for the inspection of the role of spin-orbit coupling and the resulting Rashba effect on the systems. We detail the approaches used in the code, so that it can be further exploited and adapted to other problems, such as adding new materials and functionalities which can strength the initial code scopes. Program summaryProgram title: BinPoCPC Library link to program files:https://doi.org/10.17632/zk4xy7vfy4.1Developer's repository link:https://github.com/emanuelm33/BinPoCode Ocean capsule:https://codeocean.com/capsule/0987578Licensing provisions: GPLv3Programming language: PythonExternal routines/libraries: NumPy, SciPy, Matplotlib, ASE.Nature of problem: Compute the band structure and other electronic properties in two-dimensional electron systems.Solution method: Construction of a slab Hamiltonian from one built using a basis of maximally localized Wannier functions. Solve the Schrödinger-Poisson scheme to get the self-consistent potential energy along the slab. Use this potential to compute the band structure and additional properties by solving the Schrödinger equation.Additional comments including restrictions and unusual features: Other features included are the visualization of the self-consistent process and final solutions, band structure and energy slices with different projections. High resolution and customizable figures can be obtained in all cases.

Spin and orbital magnetism of exohedral fullerene doped with single transition metal atom (Sc-Ni): A relativistic density functional theory study

Relativistic density functional theory calculations have been implemented to study the structural configurations, electronic and magnetic properties of exohedral 3d transition metal atoms doping on C60 fullerene (TM-C60) by a full potential local orbital method. The calculated binding energies revealed that the TM-C60 molecules are energetically stable in all adsorption sites. We also found that the TM-doped exohedral C60 complexes are more reactive than pure C60 fullerene. The spin and orbital magnetic moments were also determined. We have indicated that in all of the five adsorption sites, exohedral TM-C60 molecules (except for Ni-C60) are magnetized. Our magnetic calculations show that the total spin magnetic moments of TM-C60 molecules mainly come from the TM atoms. We found that the spin magnetic moments of adsorbed TM atoms in exohedral doping C60 fullerene from Sc to Mn (HH adsorption site) and for Sc to Cr (HP and P adsorption sites) are greater than their free states. Our calculations suggest that exohedral doping 3d TM-C60 complexes can almost maintain spin magnetic moments. We have indicated that the magnetic properties of exohedral TM-C60 molecules change in the presence of spin–orbit coupling. Significant orbital contributions to magnetic moments are recognized in these configurations while the spin moments are unaffected. We found that Co in exohedral doping of C60 fullerene shows a robust orbital moment in all the five adsorption sites.

Theoretical Investigation of Catalytic Water Splitting by the Arene-Anchored Actinide Complexes.

Actinide complexes, which could enable the electrocatalytic H2O reduction, are not well documented because of the fact that actinide-containing catalysts are precluded by extremely stable actinyl species. Herein, by using relativistic density functional theory calculations, the arene-anchored trivalent actinide complexes (Me,MeArO)3ArAn (marked as [AnL]) with desirable electron transport between metal and ligand arene are investigated for H2 production. The metal center is changed from Ac to Pu. Electron-spin density calculations reveal a two-electron oxidative process (involving high-valent intermediates) for complexes [AnL] (An = P-Pu) along the catalytic pathway. The electrons are provided by both the actinide metal and the arene ring of ligand. This is comparable to the previously reported uranium catalyst (Ad,MeArO)3mesU (Ad = adamantine and mes = mesitylene). From the thermodynamic and kinetic perspectives, [PaL] offers appreciably lower reaction energies for the overall catalytic cycle than other actinide complexes. Thus, the protactinium complex tends to be the most reactive for H2O reduction to produce H2 and has the advantage of its experimental accessibility.

Design of High‐Temperature Syntheses on the Example of the Heavy‐Atom Cluster Compound Sn[PtBi6I12

AbstractInvestigations into potential topological materials yielded the new subiodide Sn[PtBi6I12]. The combination of thermal analyses with phase analyses of the products of isothermal ex situ syntheses allowed the establishment of a complex high‐temperature synthesis protocol for the crystal growth of the target phase despite the lack of knowledge of the quaternary phase diagram. A special challenge was to prevent the formation of competing compounds of the solid solution series (Bi2xSn1–3x)[PtBi6I12] with x≠0. Sn[PtBi6I12] crystallizes, isostructural to Pb[PtBi6I12], in the rhombohedral space group R with lattice parameters a=1583.2(2) pm and c=1089.70(10) pm. The compound consists of cuboctahedral [PtBi6I12]2− clusters and Sn2+ cations in an octahedral coordination between the trigonal faces of two cluster units, thereby concatenating them into infinite linear chains. The chains are connected via Bi I inter‐cluster bridges, creating a high‐entropy variant of the NaCl structure type. Sn[PtBi6I12] is a semiconductor with an experimental bandgap of 0.8(1) eV. Fully relativistic density functional theory calculations including an implementation of the bifunctional formalism for the exchange energy indicate a topologically trivial bandgap of 0.81 eV between bands that are dominated by contributions of bismuth and iodine.

Bonding situation in isolable silver(I) carbonyl complexes of the Scorpionates.

The bonding situation of Ag(I)CO complexes having a Scorpionate ligand directly attached to the transition metal has been analyzed in detail by means of relativistic density functional theory calculations. To this end, different experimentally characterized complexes together with other representative species have been considered to rationalize the observed shift of the corresponding ν(CO) stretching frequencies and the influence of the substituents in the Scorpionate ligand. With the help of the energy decomposition analysis method combined with the natural orbital for chemical valence it is found that the main contribution to the bonding comes from the electrostatic attractions between the LAg(I) and CO fragments. Despite that, the LAg→CO π-backdonation is also significant in these species as well as in related LCu(I)CO complexes.