Relativistic DFT Calculations Research Articles

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 first step for the process of their disruption. 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 oxidizing agent because of its biological role as 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 wererationalized through activation strain analysis and energy decomposition analysis in the framework of scalar relativistic DFT calculations at ZORA-M06/TZ2P ae // ZORA-BLYP-D3(BJ)/TZ2P. CCCCis 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; but 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 trigger for ligand dissociation, possibly leading to metal ejection.

Axial–Equatorial Halide Ordering in Layered Hybrid Perovskites from Isotropic–Anisotropic 207Pb NMR

AbstractBandgap‐tuneable mixed‐halide 3D perovskites are of interest for multi‐junction solar cells, but suffer from photoinduced spatial halide segregation. Mixed‐halide 2D perovskites are more resistant to halide segregation and are promising coatings for 3D perovskite solar cells. The properties of mixed‐halide compositions depend on the local halide distribution, which is challenging to study at the level of single octahedra. In particular, it has been suggested that there is a preference for occupation of the distinct axial and equatorial halide sites in mixed‐halide 2D perovskites. 207Pb NMR can be used to probe the atomic‐scale structure of lead‐halide materials, but although the isotropic 207Pb shift is sensitive to halide stoichiometry, it cannot distinguish configurational isomers. Here, we use 2D isotropic–anisotropic correlation 207Pb NMR and relativistic DFT calculations to distinguish the [PbX6] configurations in mixed iodide–bromide 3D FAPb(Br1−xIx)3 perovskites and 2D BA2Pb(Br1−xIx)4 perovskites based on formamidinium (FA+) and butylammonium (BA+), respectively. We find that iodide preferentially occupies the axial site in BA‐based 2D perovskites, which may explain the suppressed halide mobility.

Axial-Equatorial Halide Ordering in Layered Hybrid Perovskites from Isotropic-Anisotropic 207 Pb NMR.

Bandgap-tuneable mixed-halide 3D perovskites are of interest for multi-junction solar cells, but suffer from photoinduced spatial halide segregation. Mixed-halide 2D perovskites are more resistant to halide segregation and are promising coatings for 3D perovskite solar cells. The properties of mixed-halide compositions depend on the local halide distribution, which is challenging to study at the level of single octahedra. In particular, it has been suggested that there is a preference for occupation of the distinct axial and equatorial halide sites in mixed-halide 2D perovskites. 207 Pb NMR can be used to probe the atomic-scale structure of lead-halide materials, but although the isotropic 207 Pb shift is sensitive to halide stoichiometry, it cannot distinguish configurational isomers. Here, we use 2D isotropic-anisotropic correlation 207 Pb NMR and relativistic DFT calculations to distinguish the [PbX6 ] configurations in mixed iodide-bromide 3D FAPb(Br1-x Ix )3 perovskites and 2D BA2 Pb(Br1-x Ix )4 perovskites based on formamidinium (FA+ ) and butylammonium (BA+ ), respectively. We find that iodide preferentially occupies the axial site in BA-based 2D perovskites, which may explain the suppressed halide mobility.

Structure and bonding in rhodium coordination compounds: a 103Rh solid-state NMR and relativistic DFT study.

This study demonstrates the application of 103Rh solid-state NMR (SSNMR) spectroscopy to inorganic and organometallic coordination compounds, in combination with relativistic density functional theory (DFT) calculations of 103Rh chemical shift tensors and their analysis with natural bond orbital (NBO) and natural localized molecular orbital (NLMO) protocols, to develop correlations between 103Rh chemical shift tensors, molecular structure, and Rh-ligand bonding. 103Rh is one of the least receptive NMR nuclides, and consequently, there are very few reports in the literature. We introduce robust 103Rh SSNMR protocols for stationary samples, which use the broadband adiabatic inversion-cross polarization (BRAIN-CP) pulse sequence and wideband uniform-rate smooth-truncation (WURST) pulses for excitation, refocusing, and polarization transfer, and demonstrate the acquisition of 103Rh SSNMR spectra of unprecedented signal-to-noise and uniformity. The 103Rh chemical shift tensors determined from these spectra are complemented by NBO/NLMO analyses of contributions of individual orbitals to the 103Rh magnetic shielding tensors to understand their relationship to structure and bonding. Finally, we discuss the potential for these experimental and theoretical protocols for investigating a wide range of materials containing the platinum group elements.

Theoretical predictions of properties and adsorption behaviour of group 1 and 2 elements, including elements 119 and 120, on hydroxylated quartz surfaces from periodic DFT calculations

Adsorption properties of group 1 and 2 elements Cs, Fr and E119 and Ba, Sr and E120, respectively, and of group 1 hydrides and hydroxides on hydroxylated quartz surfaces were calculated using a periodic relativistic DFT approach. The results show that all the considered group 1 and 2 elements should adsorb rather moderately on the quartz surfaces, with E119 and E120 most weakly, due to the strong relativistic stabilisation and contraction of the 8s atomic orbital. This means that E119 and E120 should have a deposition peak in the quartz chromatography column with a temperature gradient from room temperature to far below zero in the sequence Cs/Ba > Fr/Ra > E119/E120. For group 1 element MH and MOH, the adsorption energies are high, so that the adsorption–desorption equilibrium should be reached at very high temperatures, with the following trend in the adsorption strength MH > MOH >> M. Relativistic periodic DFT calculations of the adsorption properties of group 1 and 2 elements, including elements 119 and 120, and of their hydrides and hydroxides, on the hydroxylated quartz surfaces.

The nature of the central halide encapsulation in bambusuril hosts (BU[6]). Structural and interaction energy insights in BU[6]·X− (X = Cl, Br, I) from relativistic DFT calculations

Insights into host–guest complexation is a relevant issue towards the formation of efficient supramolecular arrays. Here, we explore the favorable encapsulation of halide anions in the representative bambus[6]uril host, with properties contrasting to the well explored in the cucurbituril family. Bambus[6]uril enables a positively charged cavity supporting the encapsulate halide ions at the center of the structure via 12C-H···X− hydrogen bonds interactions (X = F, Cl, Br and I). Our results unravel the nature of such interaction where both electrostatic and Pauli repulsion terms are relevant in the efficient encapsulation, with an increasing contribution of the orbital term for the iodine counterpart. The dispersion term contributes to a lesser extent, in contrast to the cucurbituril case. From fluorine to iodine, the contribution of different dipole–dipole interactions becomes more relevant, in agreement to the softer character of the host. Moreover, a sizable encapsulation barrier is found for F− and Cl− cases, which requires to be overwhelmed to ensure central coordination, leading to an overall bond dissociation energy (BDE) in the order Br− ∼ I− > Cl− > F−, in agreement to the experimental trend. In addition, only BU[6]·I− pair appears with a packing coefficient (PC) within the suggested favorable range (PC = 55–68%), which favors its larger aggregation constant found experimentally. A host structure breathing is suggested between D3d ↔ C1 structures, providing a flexible cavity in the bambusuril family able to maximize host–guest interactions, as observed in the case of BU[6]·I−.

Exploring the structure of halomethanes with xenon: An NMR and MD investigation

The liquid structure of dihalomethanes (CH2X2, X = Cl, Br, I) loaded with xenon gas was investigated both experimentally, by 129Xe NMR Spectroscopy, and computationally, by molecular dynamics (MD) simulations and relativistic DFT calculations. The chemical shifts of xenon have been measured in a wide range of temperatures; in addition, the spin-lattice relaxation times, T1, and the diffusion coefficients of dissolved xenon were also determined. The MD simulations of the three dihalomethanes with xenon dissolved were used to generate a collection of clusters, representing xenon with its first solvation shell, which was subsequently submitted to the relativistic DFT calculation of the 129Xe NMR shielding constant. This was finally averaged over the trajectory to obtain the corresponding chemical shift at various temperatures. The experimental data were then rationalized in terms of the density of the bulk phase and the average orientation of the halogens with respect to the xenon atom. Diffusion coefficients were also obtained from the MD simulations and compared with the experimental values, showing a good agreement.

On the Cation-π capabilities of infinitene (∞). Evaluation of bonding and circular dichroism properties for Infinitene-Ag(I)n (n = 1–4) complexes from relativistic DFT calculations

The helicoidal π-conjugated structure from helicenes is able to feature cation-π bonding towards Ag(I) atoms, resulting in the variation of their inherent high optical rotation values. Recently, the characterization of infinitene ([12]infinitene) as two fused [6]helicene structures with a central crossover section suggests the extension of such coordination characteristics to large and more complex structural landscapes. Herein, we evaluated the possible cation-π features of infinitene towards one to four silver cations from density functional calculations and their role in the optical rotation of the infinity-shaped backbone. The nature of the cation-π interaction for infinitene, shows a favorable formation of single and multiple Ag(I) aggregation, with a slight distortion of the structural backbone. Hence, the formation of cation- π complexes in infinitene is plausible, suggesting the expansion of its chemistry towards the formation of metal complexes in fused helicene species.

Nature and role of formal charge of the ion inclusion in hexanuclear Platinum(II) Host-Guest Species. Insights from relativistic DFT calculations

The favorable formation of [Pt6(SR)12 ⊃ Ag]+ host–guest species exhibits the ability of the [Pt6(SR)12] host to incorporate metallic ions at the inner cavity, offering an interesting template for further evaluation of the ion-inclusion nature. Our results show a sizable interaction of −129.1 kcal·mol−1 between Ag(I) and [Pt6(SR)12], of mainly charge-transfer (covalent) character, followed by a contribution from its electrostatic character, and to a small extent from London dispersion type interactions, larger than evaluated for organic hosts. The proposed Cu(I) and Au(I) species exhibit enhanced interaction energy, suggesting the plausible formation of host–guest pairs along with the coinage metal group.Furthermore, the role of the metallic ion charge shows that a more positive formal charge of the ion (Zn(II), Cd(II), and Hg(II)), leads to a sizable stabilization, owing to the increase of the charge-transfer (covalent) character of the interaction, In contrast, for neutral species (Ni, Pd, Pt), a sizable decrease of such character is calculated, denoting that the formal charge of the ion is a relevant factor in determining the stabilization of the host–guest interaction, suggesting to the inclusion of relevant metals ions from different groups, leading to particular optical absorption patterns.

Formation of C60-SnI4 adducts. Insights of the role of σ-hole and tetrel-bonding in the strength and interaction nature from DFT calculations

C60-SnI4 cocrystals expose the ability of highly symmetric units to form chiral materials. Here, we explore the underlying characteristics accounting for the stabilization of the C60•••SnI4 interaction within the framework of relativistic dispersion-corrected DFT calculations. Our results explore different interaction modes ranging from a purely σ -bond to tetrel-bond for C60•••SnI4 denoting the larger contribution from London-type interaction being more relevant than the electrostatic character inherent to σ-hole interactions, owing to the presence of iodine atoms. The resulting aggregate is further evaluated owing to its structural flexibility given by different noncovalent interaction modes based on both σ -hole and tetrel-bonding characteristics of SnI4. Hence, it is proposed that C60-SnI4 cocrystals can be further modified under compression undergoing different phase transitions, leading to further exploration of crystal characteristics and versatility, which may be extended to other interesting π-systems. In addition, C60-EX4 (E = C, Si, Ge, Sn, Pb; X = Cl, Br, I) series are given, showing similar stabilizing characteristics, increasing towards heavier elements, denoting the C60-PbI4 cocrystal as a noteworthy case with stronger noncovalent interactions, which is here encouraged for further explorations.

Reactivity of Group 13 Elements Tl and Element 113, Nh, and of Their Hydroxides with Respect to Various Quartz Surfaces from Periodic Relativistic DFT Calculations.

Adsorption properties of group 13 element Tl and the superheavy element Nh, as well of their hydroxides on various modified quartz surfaces, are predicted on the basis of relativistic periodic DFT calculations using the BAND software. The obtained adsorption energies, Eads, of the MOH (M = Tl and Nh) molecules are indicative of the relatively strong interaction of the hydroxides with all the considered quartz surfaces. In contrast, adsorption of the Tl and Nh atoms was found to be significantly weaker. The adsorption strength of both M and MOH (M = Tl and Nh) was shown to increase with the dehydroxylation of the quartz surface. Very good agreement is reached between the calculated Eads(TlOH) of 133 kJ/mol on the fully hydroxylated quartz surface and of 157 kJ/mol on the partially dehydroxylated quartz surface on the one hand and experimental adsorption enthalpies, -ΔHads, of 134/137 ± 5 kJ/mol (at ∼300 °C) and 158 ± 3 kJ/mol (at ∼500 °C), respectively, on the other hand. Thus, we suggest that all the experimental ΔHads values for Tl should be assigned to the adsorption/desorption of the TlOH molecule. For NhOH, its adsorption properties on various quartz surfaces should be very similar to those of TlOH, with slightly smaller Eads values. Adsorption of the Nh atom should, however, be much weaker than that of the Tl atom due to stronger spin-orbit effects in Nh.

Vibrational Corrections to NMR Spin-Spin Coupling Constants from Relativistic Four-Component DFT Calculations.

Zero-point vibrational (ZPV) corrections to the nuclear spin–spin coupling constants have been calculated using four-component Dirac–Kohn–Sham DFT for H2X (where X = O, S, Se, Te, Po), XH3 (where X = N, P, As, Sb, Bi), and XH4 (where X = C, Si, Ge, Sn, and Pb) molecules and for HC≡CPbH3. The main goal was to study the influence of relativistic effects on the ZPV corrections and thus results calculated at relativistic and nonrelativistic approaches have been compared. The effects of relativity become notable for the ZPV corrections to the spin–spin coupling constants for compounds with lighter elements (selenium and germanium) than for the spin–spin coupling constants themselves. In the case of molecules containing heavier atoms, for instance BiH3 and PbH4, relativistic effects play a crucial role on the results and approximating ZPV corrections by the nonrelativistic results may lead to larger errors than omitting ZPV corrections altogether.

DFT study of honeycomb Sb layers on the Ag(111) surface

The electronic structure of the Sb layer on Ag(111), recently reported to have a flat (√3 × √3) honeycomb structure similar to that of graphene [Y. Shao et al., Nano Lett. (2018) 18:2133–9], is studied by means of relativistic DFT calculations. In accordance with earlier results, a flat free Sb monolayer is found to be metastable, as follows from the existence of an imaginary phonon mode. The layer spontaneously reconstructs into a buckled honeycomb structure, which leads to the metal-to-nonmetal transition. It is suggested therefore that the formation of a flat Sb honeycomb layer becomes possible just because of the substrate-induced tensile strain, which results in the stabilization of the structure. The binding (adsorption) energy per Sb atom for the honeycomb structure is found to be rather strong, 4.61 eV, which can be explained by a significant lateral attraction between Sb adatoms. The formation of the honeycomb structure and its stability are studied by performed Monte Carlo simulations within the lattice-gas model either with account for trio interactions, or with some effective energy parameters. The SOC only slightly changes the band structure of the system, but, due to pronounced downward shift of the cone-like band in vicinity of K point, leads to the second surface band crossing EF. A detailed analysis of the localization of the wave functions indicates that the bands crossing EF loose the surface weight away from K point, so that they are not localized in the Sb adlayer in the net Brillouin zone.

Silver(I) and gold(I) complexes with bitriazole‐based N‐heterocyclic carbene ligand: Solid state features and behaviour in solution

AbstractThe coordinating properties of the bis(1,4‐dimethyl‐1,2,4‐triazol‐5‐ylidene) ligand (abbreviated as bitz) towards silver(I) and gold(I) centres have been explored. The bitz behaves as bridging ligand giving both dinuclear [M2(bitz)2](PF6)2 and trinuclear [M3(bitz)3](PF6)3 species, whose formation has been supported by X‐ray diffraction analysis, NMR spectroscopy and mass spectrometry evidences. The dinuclear and trinuclear gold(I) complexes present very similar luminescence properties, emitting in the blue region, at ~450 nm, when excited at 350 nm. Selected experimental aspects dealing with the synthesis of the dinuclear and trinuclear species, as well as with the absorption properties of the gold(I) complexes, have been investigated also through relativistic DFT calculations.

Indenyl and Allyl Palladate Complexes BearingN‐Heterocyclic Carbene Ligands: an Easily Accessible Class of New Anticancer Drug Candidates

AbstractThe mechanochemical syntheses of allyl and indenyl palladate complexes are reported. All compounds were obtained in quantitative yields and microanalytically pure without the need of any workup. These complexes are stable in chlorinated and polar (DMSO or DMSO/H2O solutions) solvents. In chlorinated solvents, they appear as ionic pairs of which crystals suitable for single X‐ray diffraction studies have been obtained. Bonding and solvation properties are rationalized through scalar relativistic DFT calculations. Moreover, most complexes showed excellent cytotoxicity towards ovarian cancer cell lines, with IC50values comparable or lower than cisplatin. The potent anticancer activity of two IPrCland IPr*‐based palladate complexes was examined in a high‐grade serous ovarian cancer (HGSOC) patient‐derived tumoroid. Moreover, the inhibition of the antioxidant enzyme thioredoxin reductase (TrxR) was noticed, and structure‐activity relationships could be derived, suggesting the ROS detoxifying system is involved in the mode of action.

DFT study of Sb layers on the Mo(112) surface

Relativistic DFT calculations, performed for Sb layers adsorbed on the Mo (112) surface, have revealed a strong interaction of Sb adatoms with the surface. At low coverages, the layer is predicted to form a c (2 × 2) structure, while for a complete Sb monolayer the most favorable structure is the p (1 × 1), which forms despite a minor one-dimensional compressing of the layer in the direction along the Mo (112) surface furrows. This structure is favorable also for complete bilayer and 3-layer films, so that very thin Sb layers reproduce the furrowed structure of the Mo (112) surface. The adsorbed Sb layers cause a significant redistribution of the densities of states, which, however, does not increase enough at the Fermi level to produce any substantial metallization of the film. The spin-orbit coupling causes only minor changes in the band structure, while Sb layer on one face of the Mo (112) slab destroys the inversion symmetry of the adsorption system thus leading to the appearance of the Rashba-type splitting of the bands.

New Hypercoordinating Organostannanes for the Modular Functionalization of Mono‐ and Polystannanes: Synthetic and Computational Studies**

AbstractA series of potentially hypercoordinate tin compounds derived from a substitutionally labile tosyl stannane (5) was produced to gain access to a library of propyloxybiphenyl (11), propylmethoxy (12, 14, 18, 22) or propylthioester (13, 15, 19, 23) stannanes for structure/property/polymerization investigations. Structural characterizations by single crystal X‐ray diffraction of 12, 14, 18 and 19 were also undertaken. The relative energies of hypercoordinate conformers for the propylmethoxystannanes 12, 14, 18, and 22 were determined with DFT methods and the fractional abundance of conformers in the gas and solution (CHCl3) phase were estimated. Relativistic DFT calculations of 119Sn NMR chemical shifts were carried out for a series of non‐hypercoordinate reference compounds and the conformers, allowing the estimation of Boltzmann‐averaged chemical shifts of the hypercoordinate propylmethoxystannanes. A semi‐crystalline homopolymer (25) was isolated from the dehydropolymerization of 22 using Wilkinson's catalyst. Conversion of the liable tosylated polystannane (24) to a new partially substituted polystannane (28) via nucleophile displacement reactions was achieved.

Nature and Role of Formal Charge of the Ion Inclusion in Hexanuclear Platinium(Ii) Host-Guest Species. Insights from Relativistic Dft Calculations

Nature and Role of Formal Charge of the Ion Inclusion in Hexanuclear Platinium(Ii) Host-Guest Species. Insights from Relativistic Dft Calculations

Reactivity of superheavy elements Cn and Fl and of their oxides in comparison with homologous species of Hg and Pb, respectively, towards gold and hydroxylated quartz surfaces.

Adsorption energies, Eads, and other properties of atoms and oxides of the superheavy elements (SHEs) Cn and Fl, as well as of the homologous species of Hg and Pb, on Au(111) and fully hydroxylated quartz surfaces are predicted on the basis of 2c-DFT calculations and a periodic slab model using BAND software. The ambition of the work is to interpret the outcome of "one-atom-at-a-time" gas-phase chromatography experiments on the reactivity/volatility of SHEs. The present results with an improved (dispersion corrected) exchange-correlation functional show that, in agreement with our earlier predictions and experimental results on Pb, Hg and Cn, the sequence of the Eads values of the atoms on the gold surface should be Pb ≫ Hg > Fl > Cn, with rather moderate Eads values smaller than 90 kJ mol-1 (except for that for Pb). Oxides of Hg, Cn and Fl should be much more reactive with the gold surface than the corresponding atoms, with Eads values of about 200 kJ mol-1. A striking difference in the geometry of the deposited oxides was found between group 12 and group 14. An analysis of the Eads values for M and MO (M = Hg/Cn and Pb/Fl) on the hydroxylated α-quartz surface enables one to conclude that atoms of Hg, Cn and Fl should not interact with such a surface at room temperature, while Pb should adsorb on it. Oxides of these elements, on the contrary, should strongly adsorb on quartz with Eads ≥ 100 kJ mol-1. The present theoretical data agree with the experimental results on the elemental species of Hg, Cn and Fl.

Metallaaromaticity - a protean world.

The nature of magnetically induced current densities (MICD) of metallabenzenes and related compounds has been examined with relativistic DFT calculations to assess the magnetic aromaticity of the molecules. The origin of the total MICD has been analyzed in terms of individual molecular orbital (MO) contributions. Our study reveals that the σ-framework of the molecules always makes a diamagnetic contribution to the MICD. On the other hand, π-MOs and Craig-Möbius type π-MOs, i.e., MOs in which the dxy/dxz orbitals of the metal centers change the phase of the wave function akin to a Möbius twist, may not make a diatropic contribution. We have identified metallabenzenes with multiple magnetic aromaticities. In the case of iridabenzenes, σ-MICD has been found to decrease dramatically from Ir(III) to Ir(V) systems. Furthermore, a brief examination of some recently synthesized metallapolycycles has shown that the metal center in a given ring can strongly modulate the aromaticity of neighboring rings. Finally, the finding that relatively minor perturbations in the ligand environment of the metal can substantially influence the aromaticity of metallabenzenes and related molecules underscores the protean character of metallaaromaticity and the need for even wider-ranging investigations. Considering the conflicts between magnetic response and ground-state aromaticity criteria (energetic, structural, and electronic criteria), we propose that the term aromatic be used for labeling a molecule if and only if all criteria confirm aromaticity. In other words, neither magnetic nor ground-state criteria are necessary and sufficient conditions for labeling a molecule aromatic.