Relativistic DFT Research Articles

Hyperfine Effects in Ligand NMR: Paramagnetic Ru(III) Complexes with 3-Substituted Pyridines.

NMR spectroscopy is an indispensable tool in characterizing molecular systems, including transition-metal complexes. However, paramagnetic transition-metal complexes such as those with ruthenium in the +3 oxidation state are troublemakers because their unpaired electrons induce a fast nuclear spin relaxation that significantly broadens their NMR resonances. We recently demonstrated that the electronic and spin structures of paramagnetic Ru(III) systems can be characterized in unprecedented details by combining experimental NMR results with relativistic density-functional theory ( Novotny et al. J. Am. Chem. Soc. 2016 , 138 , 8432 ). In this study we focus on paramagnetic analogs of NAMI with the general structure [3-R-pyH]+trans-[RuIIICl4(DMSO)(3-R-py)]-, where 3-R-py stands for a 3-substituted pyridine. The experimental NMR data are interpreted in terms of the contributions of hyperfine (HF) NMR shielding and the distribution of spin density calculated using relativistic DFT. The DFT computational methodology is evaluated, and the effects of substituents, environment, and relativity on the hyperfine shielding are discussed. Particular attention is paid to the analysis of the fundamental Fermi-contact (FC), spin-dipole (SD), and paramagnetic spin-orbit (PSO) terms that contribute to the hyperfine 1H and 13C NMR shifts of the individual atoms in the pyridine ligands and the spin-polarization effects in the ligand system that are linked to the character of the metal-ligand bond. The individual HF shielding terms are systematically discussed as they relate to the traditional, but somewhat mixed, contact and pseudocontact NMR contributions used extensively by experimental spectroscopists in biomolecular NMR and the development of PARACEST magnetic-resonance contrast agents.

Four-Component Relativistic Density Functional Calculations of EPR Parameters for Model Complexes of Tungstoenzymes

For a closer validation of four-component relativistic DFT methods within the matrix Dirac-Kohn-Sham (mDKS) framework with global hybrid functionals for EPR parameter calculations to be applied in the modeling of tungsten enzymes, we refine a previously suggested protocol for computations on 5d systems. This is done for a series of larger, unsymmetrical W(V) complexes thought to closely resemble enzyme active sites in this oxidation state. Particular focus is placed on complexes with thiolate and dithiolene ligands, along with an evaluation of the influence of different amounts of exact-exchange incorporated in hybrid PBE0-xHF functionals, an implicit solvent model, and structural changes on the computed EPR parameters. Compared to previous work, a slightly modified protocol with different optimal exact-exchange admixtures for electronic g- and hyperfine A-tensors is found to provide the best agreement with experimental EPR data. It will provide the basis for our subsequent tungsten enzyme modeling efforts.

A First-Principles Calculation of Electronic Structure and dHvA Simulation of the Novel Superconductor Re6Hf

In this paper, we performed a density functional theory calculation study on the newly discovered superconductor Re6Hf containing anti-symmetric spin-orbit coupling (ASOC) properties. The calculated densities of electronic states demonstrate that the d–d interaction of Re6Hf is much stronger than that in Re6Zr. A fully relativistic DFT study shows a special performance of densities of states for the spin-up and spin-down electrons. Band structure calculations indicate that the lifting at several high symmetric k points and plenty of splits in band structures yield significant topological transitions in the Fermi surfaces of Re6Hf. The energy splitting of bands caused by ASOC are estimated to be 34 and 44 meV, respectively. The de Hass-van Alphen effect simulation is demonstrated and analyzed.

Eclipsed- and Staggered-[Ge18Pd3{EiPr3}6]2- (E = Si, Sn): Positional Isomerism in Deltahedral Zintl Clusters.

We report the synthesis and characterization of the cluster anions [Ge18Pd3{SiiPr3}6]2- (1) with a core of face-fused twinned icosahedra, Ge18Pd3, and two sets of three iPr3Si-substituents positioned in "eclipsed" geometry. The new anion is a positional isomer of the recently reported "staggered" stannyl-ligated counterpart [Ge18Pd3{SniPr3}6]2- (2), showing the possibility to find such positional isomerism in Zintl clusters. Both anions are characterized by single-crystal X-ray diffraction, 1H and 13C NMR, and negative-ion ESI-MS. Using relativistic DFT calculations, we elucidate and discuss the reasons for the different positioning of the ligands in the stannyl- and silyl-functionalized species.

Synthesis, characterization and relativistic DFT studies of fac-Re(CO)3(isonicotinic acid)2Cl complex

In this work, new fac-Re(CO)3(PyCOOH)2Cl from isonicotinic acid ligand has been prepared. The complex was characterized by structural (single-crystal X-ray diffraction), elemental analysis and spectroscopic (FTIR, NMR, UV–vis spectroscopy) methods. DFT and TDDFT calculations were performed to obtain the electronic transitions involved in their UV–Vis spectrum. The excitation energies agree with the experimental results. The TDDFT calculations suggest that experimental mixed absorption bands at 270 and 314 nm could be assigned to (MLCT-LLCT)/MLCT transitions. Natural Bond Orbitals (NBO) approach has enabled studying the effects of bonding interactions. E(2) energies confirm the occurrence of ICT (Intra-molecular Charge Transfer) within the molecule.

Pacman‐Like Alkaliated Actinyl Complexes of a Polypyrrolic Macrocycle: A Relativistic DFT Study

AbstractA series of doubly alkaliated actinyl complexes, [(thf)(AnmO2)(A2L)]n– (Anm‐A; An=U, Np and Pu; m=VI and n=0; m=V and n=1; A=Li, Na and K; L is an octadentate polypyrrolic tetraanion) have been investigated for their structures, transformation reaction energies and redox property using relativistic density functional theory. The study confirms experimental results of the synthesized lithiated uranyl complexes and the proposed potassiated uranyl ones, and furthermore extends to more toxic and radioactive transuranics that are difficultly handled in experiment. Comparison with hydrogen analogues, [(thf)(AnmO2)(H2L)]n– (Anm‐H), finds that the introduction of alkali atoms lengthens An=Oendo and An=Oexo bonds. Transformation reaction of Anm‐A (A=Li, Na and K) starting from the respective Anm‐H was calculated to be exothermic. The alkaliated complex shows more positive reduction potential in most cases. All the results unravel the alkali‐mediated activation on the inert uranyl(VI) U=O bonding; the lithium complex, for instance, possesses the largest reduction potential (E0corr), which indicates the strongest lithium activation. Further comparison was also made with the alkaliated uranyl complexes where the alkali metals are saturated by thf molecules.

Exploring the geometrical and optical properties of neutral rhenium (I) tricarbonyl complex of 1,10-phenanthroline-5,6-diol using relativistic methods

In this contribution, we studied through experimental and relativistic DFT (R-DFT) calculations, the neutral complex fac-[Re(CO)3(1,10-phenanthroline-5,6-diol)Cl] (B1) as a potential precursor compound for designing new fluorophores suitable for confocal microscopy specially in walled cells. This work also describes via DFT calculations the electronic and spectroscopic properties of the facial (fac) and meridional (mer) isomers of this compound. The calculations shows that mer-isomer is 17.5kcal/mol (in vacum) and 21.1kcal/mol (when the solvent is considered) higher in energy with respect to the fac-isomer. The calculated emission spectra of B1, indicates an emission around 620nm in acetonitrile in good agreement with the experimental reports for similar molecules. Finally, the Morokuma–Ziegler energy decomposition analysis shows a major lability for Cl ligand which is ideal for designing new compounds replacing this ligand for another ancillary ligand suitable for biological applications.

Coinage Metal Superatomic Cores: Insights into Their Intrinsic Stability and Optical Properties from Relativistic DFT Calculations.

Coinage-metal atomically precise nanoclusters are made of a well-defined metallic core embedded in a ligand-protecting outer shell. Whereas gold derivatives are particularly well documented, examples of silver nanoclusters are somewhat limited and copper species remain particularly scare. Our DFT relativistic calculations on superatomic metallic cores indicate that copper species are almost as stable as gold clusters and more stable than their silver counterparts. Thus, for silver superatomic cores, the role of the stabilizing ligands is more crucial in the stabilization of the overall structure, in comparison to copper and gold. Hence, the chemistry of the earlier counterparts of gold, especially copper, should grow quickly with at least characterizations of species related to that found in the heavier elements in the triad, which requires tackling synthetic challenges. Time-dependent (TD)-DFT calculations show that with an increase of the cluster core nuclearity, the absorption bands are redshifted, allowing us to differentiate between the clusters types. Moreover, the optical properties of the silver cores are fairly different from that of their Cu and Au relatives.

DFT and Monte Carlo study of the W(001) surface reconstruction

The driving force for the W(001) surface reconstruction and electronic structures of pristine and H-covered W(001) surfaces are studied by means of relativistic DFT calculations. The spin-orbit coupling leads to the splitting of the bands. Adsorbed physical monolayer of hydrogen due to forming adsorption bonds stabilizes the (1 × 1) structure of the H/W(001) surface. The performed calculations have not revealed any substantial nesting of Fermi surface, so do not support the Peierls-like charge-density-wave mechanism of the surface reconstruction. The total energy of the (√2 × √2)R45° W(001) surface structure is found to be lower, by 0.14 eV per atom, than for the (1 × 1 W(001). The dependence of the relative intensity of the characteristic LEED reflection on temperature, obtained with the help of Monte Carlo simulations using the interaction energies estimated from DFT calculations, is in good agreement with available experimental data, thus supporting the concept of the order-disorder type of the transition between the low-temperature ((√2 × √2)R45° and room-temperature (1 × 1) surface structures of W(001).

X-ray diffraction and relativistic DFT studies on the molecular biomarker fac-Re(CO)3(4,4′-dimethyl-2,2′-bpy)(E-2-((3-amino-pyridin-4-ylimino)-methyl)-4,6-di-tert-butylphenol)(PF6)

The fac-[Re(CO)3(4,4′-dimethyl-2,2′-bpy)L]PF6 (C2) complex have been recently reported as a useful fluorophore for walled cells (yeasts and bacteria) without the need of antibodies. In the present work, we report the structural parameters of the C2 complex, where L is an ancillary ligand E-2-((3-amino-pyridin-4-ylimino)-methyl)-4,6-di-tert-butylphenol, which presents an intramolecular hydrogen bond (IHB). The C2 crystals were obtained by slow evaporation of a dichloromethane solution, yielding yellow blocks. The crystal structure solution of the complex C2 showed a monoclinic crystal system and discrete organometallic cations and PF6 − as the counter ion, with partially occupation of solvent molecules (CH2Cl2). The complex C2 having a fac-geometry of the three carbonyl ligands, possesses the following bond distances Re–C(CO): Re1–C24, 1.87(8) A; Re1–C25, 1.58(12) A and Re1–C26, 1.90(8) A. The distorted octahedral geometry observed in the C2 structure is due to the C(CO)–Re1–N1(imine) angle for the three carbonyls that are significantly different. The Re–N1 bond distance of 2.16(4) A corresponds to the nitrogen coordination of the pyridine fragment of the ancillary ligand L, completing the octahedral geometry. Here we complement the C2 descriptions due to the considerable biological interest of its use as d6 metal fluorophore in walled cells (i.e., yeast and bacteria). DFT calculations were performed including scalar and spin–orbit (SO) relativistic effects with agree often reasonably well with experimental X-ray data. Through frequency calculations we estimated the strength of the intramolecular hydrogen bond (with a OH···N distance of 2.621 A) accounting for near 40 kcal/mol, indicating that is a strong hydrogen bond which contributes to the molecular stability. In addition, we observed the L electron-withdrawing effect on the rhenium core. The agreement between the observed and computed bond distances and angles brings confidence on the choice of the computed models and level of theory. These kind of Rhenium (I) complexes designed to develop novel fluorophores suitable for biological applications.

Chemistry of the 5g Elements: Relativistic Calculations on Hexafluorides

A Periodic System was proposed for the elements 1-172 by Pyykkö on the basis of atomic and ionic calculations. In it, the elements 121-138 were nominally assigned to a 5g row. We now perform molecular, relativistic four-component DFT calculations and find that the hexafluorides of the elements 125-129 indeed enjoy occupied 5g states.

Metal-metal multiple bond in low-valent diuranium porphyrazines and its correlation with metal oxidation state: A relativistic DFT study

To explore the uranium-uranium bonding nature, a ligated diuranium complex that could be experimentally possible would show features with no bridging ligand constraints (i.e. discrete or unsupported ligand), rigid ligand skeleton and suitable U-ligand bond. In this respect, we have designed and examined a series of diuranium diporphyrazines (Um2Pz2, m=II, III and IV) using relativistic density functional theory. Optimizations on all possible electron-spin isomers find that the triplet, quintet and quintet states are energetically lowest for Um2Pz2 (m=II, III and IV), respectively. They possess bond lengths of UU at 2.37, 2.46 and 2.91Å, bond orders of 3.48, 3.33 and 2.11, and stretching vibrational frequencies of 239, 172 and 108cm−1. Associated with the electronic-structure and QTAIM (quantum theory of atoms in molecules) analyses, a weak quadruple bond is suggested for the triplet state of UII2Pz2, and the triple and double bonds for UIII2Pz2, and UIV2Pz2, respectively. It shows that the uranium oxidation state approximately correlates with the number of multiple bonds.

Cyanide linkage isomerism in cerium(III) and uranium(III) complexes. A relativistic DFT study

The chemistry of cyanide complexes of the f-elements has witnessed significant recent advances, showing in particular the remarkable ability of the cyanide ligand to stabilize uranium compounds in their +3 to +6 oxidation states and its capacity to adopt two distinct ligation modes, namely cyanide M−CN or isocyanide M−NC, towards trivalent f-ions. Here, we have theoretically investigated the tris(cyanide) complexes [ML2X3]2– (M = Ce3+, U3+; L = C5H4Me, N(SiMe3)2; X = CN, NC), using relativistic DFT computations, focusing on cyanide (CN−) and isocyanide (NC−) coordination competition and differences between their electronic structures. X-ray crystal data reveal distinct coordination modes of the CN ligand towards uranium and cerium metal centers. Interestingly, in the case of the cerium complexes, and contrarily to the uranium ones, the coordination mode of the cyanide ligand depends on the co-ligand L attached to the metal. The observed coordination in these tris(cyanide) complexes is driven by the binding energies of the CN−/NC− ligands to the metals. The solvent is shown to play a determining role for the chosen coordination. The developed methodology can help to confirm the cyanide or isocyanide coordination mode when X-ray crystal data are not conclusive or to predict the configuration of a complex to be synthesized. Another application is in the field of lanthanide (III)/actinide (III) differentiation.

Estimation of ΔR/R values by benchmark study of the Mössbauer Isomer shifts for Ru, Os complexes using relativistic DFT calculations

The present study applies all-electron relativistic DFT calculation with Douglas-Kroll-Hess (DKH) Hamiltonian to each ten sets of Ru and Os compounds. We perform the benchmark investigation of three density functionals (BP86, B3LYP and B2PLYP) using segmented all-electron relativistically contracted (SARC) basis set with the experimental Mössbauer isomer shifts for 99Ru and 189Os nuclides. Geometry optimizations at BP86 theory of level locate the structure in a local minimum. We calculate the contact density to the wavefunction obtained by a single point calculation. All functionals show the good linear correlation with experimental isomer shifts for both 99Ru and 189Os. Especially, B3LYP functional gives a stronger correlation compared to BP86 and B2PLYP functionals. The comparison of contact density between SARC and well-tempered basis set (WTBS) indicated that the numerical convergence of contact density cannot be obtained, but the reproducibility is less sensitive to the choice of basis set. We also estimate the values of ΔR/R, which is an important nuclear constant, for 99Ru and 189Os nuclides by using the benchmark results. The sign of the calculated ΔR/R values is consistent with the predicted data for 99Ru and 189Os. We obtain computationally the ΔR/R values of 99Ru and 189Os (36.2 keV) as 2.35×10−4 and −0.20×10−4, respectively, at B3LYP level for SARC basis set.

Interfacial Interaction of Titania Nanoparticles and Ligated Uranyl Species: A Relativistic DFT Investigation.

To understand interfacial behavior of actinides adsorbed onto mineral surfaces and unravel their structure-property relationship, the structures, electronic properties, and energetics of various ligated uranyl species adsorbed onto TiO2 surface nanoparticle clusters (SNCs) were examined using relativistic density functional theory. Rutile (110) and anatase (101) titania surfaces, experimentally known to be stable, were fully optimized. For the former, models studied include clean and water-free Ti27O64H20 (dry), partially hydrated (Ti27O64H20)(H2O)8 (sol) and proton-saturated [(Ti27O64H20)(H2O)8(H)2]2+ (sat), while defect-free and defected anatase SNCs involving more than 38 TiO2 units were considered. The aquouranyl sorption onto rutile SNCs is energetically preferred, with interaction energies of -8.54, -10.36, and -2.39 eV, respectively. Energy decomposition demonstrates that the sorption is dominated by orbital attractive interactions and modified by steric effects. Greater hydrogen-bonding involvement leads to increased orbital interactions (i.e., more negative energy) from dry to sol/sat complexes, while much larger steric interaction in the sat complex significantly reduces the sorption interaction (i.e., more positive energy). For dry SNC, adsorbates were varied from aquo to aquo-carbonato, to carbonato, to hydroxo uranyl species. Longer U-Osurf/U-Ti distances and more positive sorption energies were calculated upon introducing carbonato and hydroxo ligands, indicative of weaker uranyl sorption onto the substrate. This is consistent with experimental observations that the uranyl sorption rate decreases upon raising solution pH value or adding carbon dioxide. Anatase SNCs adsorbing aquouranyl are even more exothermic, because more bonds are formed than in the case of rutile. Moreover, the anatase sorption can be tuned by surface defects as well as its Ti and O stoichiometry. All the aquouranyl-SNC complexes show similar character of molecular orbitals and energetic order although differing in highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gaps and orbital energy levels, but changes can be accomplished by adding carbonato and hydroxo ligands.

Activation Strain Analysis of SN2 Reactions at C, N, O, and F Centers.

Fundamental principles that determine chemical reactivity and reaction mechanisms are the very foundation of chemistry and many related fields of science. Bimolecular nucleophilic substitutions (SN2) are among the most common and therefore most important reaction types. In this report, we examine the trends in the SN2 reactions with respect to increasing electronegativity of the reaction center by comparing the well-studied backside SN2 Cl– + CH3Cl with similar Cl– substitutions on the isoelectronic series with the second period elements N, O, and F in place of C. Relativistic (ZORA) DFT calculations are used to construct the gas phase reaction potential energy surfaces (PES), and activation strain analysis, which allows decomposition of the PES into the geometrical strain and interaction energy, is employed to analyze the observed trends. We find that SN2@N and SN2@O have similar PES to the prototypical SN2@C, with the well-defined reaction complex (RC) local minima and a central barrier, but all stationary points are, respectively, increasingly stable in energy. The SN2@F, by contrast, exhibits only a single-well PES with no barrier. Using the activation strain model, we show that the trends are due to the interaction energy and originate mainly from the decreasing energy of the empty acceptor orbital (σ*A–Cl) on the reaction center A in the order of C, N, O, and F. The decreasing steric congestion around the central atom is also a likely contributor to this trend. Additional decomposition of the interaction energy using Kohn–Sham molecular orbital (KS-MO) theory provides further support for this explanation, as well as suggesting electrostatic energy as the primary reason for the distinct single-well PES profile for the FCl reaction.

DFT study of electronic properties of noble d-metallic surface structures

The DFT study of electronic properties for bulk metals Au Pt and Pd, their polycrystalline films of nanometer thickness is presented. The calculations were performed using density functional theory with pseudopotential, fully relativistic DFT approximations and technique to recover density of valence states of polycrystalline structures that allow describing the experimentally observed features of valence band XPS spectra of these metals was obtained. The results of the work are suitable for accurate modeling the surface DOS of real samples together with XPS analysis.

Relativistic DFT investigation of electronic structure effects arising from doping the Au25 nanocluster with transition metals

We perform a theoretical investigation using density functional theory (DFT) and time-dependent DFT (TDDFT) on the doping of the Au25(SR)18-1 nanocluster with group IX transition metals (M = cobalt, rhodium and iridium). Different doping motifs, charge states and spin multiplicities were considered for the single-atom doped nanoclusters. Our results show that the interaction (or the lack of interaction) between the d-type energy levels that mainly originate from the dopant atom and the super-atomic levels plays an important role in the energetics, the electronic structure and the optical properties of the doped systems. The evaluated MAu24(SR)18q (q = -1, -3) systems favor an endohedral disposition of the doping atom typically in a singlet ground state, with either a 6- or 8-valence electron icosahedral core. For the sake of comparison, the role of the d energy levels in the electronic structure of a variety of doped Au25(SR)18-1 nanoclusters was investigated for dopant atoms from other families such as Cd, Ag and Pd. Finally, the effect of spin-orbit coupling (SOC) on the electronic structure and absorption spectra was determined. The information in this study regarding the relative energetics of the d-based and super-atom energy levels can be useful to extend our understanding of the preferred doping modes of different transition metals in protected gold nanoclusters.

Formation of a Trifluorophosphane Platinum(II) Complex by P-F Bond Activation of Phosphorus Pentafluoride with a Pt0 Complex.

The reaction of PF5 with [(Cy3 P)2 Pt] gave the PF3 complex trans-[(Cy3 P)2 PtF(PF3 )][PF6 ], which was characterized by single-crystal X-ray diffraction, multinuclear NMR spectroscopy, and elemental analysis. To the best of our knowledge, this reaction is the first example of the oxidative addition of a P-F bond to a transition metal and is a rare example of an activation of a main-group-element-fluorine bond by a metal. Relativistic DFT calculations showed that the formation of the Lewis pair [(Cy3 P)2 Pt→PF5 ], which was not observed even at low temperatures, represents the initial step of the reaction. From this key intermediate, the cation trans-[(Cy3 P)2 PtF(PF3 )]+ was furnished by a two-step mechanism involving, successively, a second and a third PF5 molecule.

Doping the Superatom with p-Elements: The Role of p-Block Endohedral Atoms in Bonding and Optical Properties of E@Au24(SR)18 (E = Si, Ge, Sn, and Pb) from Relativistic DFT Calculations

Expanding the versatility of well-defined clusters seeking distinctive physical and chemical behavior in a rational manner is a relevant issue in the design of functional nanostructures. Superatomic clusters through the prominent Au25(SR)18 aggregate offer an ideal template and robust framework to gain understading of the different behavior gained by the inclusion of different endohedral dopant atoms. Our results allow to gain more insights into the role of group XIV elements for both optical and bonding, revealing characteristic patterns to be expected in their low-energy UV-spectrum. The bonding shows an extension of the regular s-type interaction observed in [Au@Au24(SR)18]− to a more extended and covalent interaction given by s- and p-type interaction when the central atom is replaced by a group XIV elements, which can be expected of other endohedral p-block elements. In addition, the role of the spin–orbit coupling into the electronic and optical properties is discussed in terms of the new selection rules required by such regime. The characteristic optical and bonding patterns resulting from the p-element endohedral doping of the Au25(SR)18 superatom shed light into the rational variation of the molecular properties upon inclusion of an endohedral p-block element.