Exploring the impact of alignment media on RDC analysis of phosphorus-containing compounds: a molecular docking approach.

Residual dipolar couplings (RDCs) are employed in NMR analysis when conventional methods, such as J-couplings and nuclear Overhauser effects (NOEs) fail. Low-energy (optimized) conformers are often used as input structures in RDC analysis programs. However, these low-energy structures do not necessarily resemble conformations found in anisotropic environments due to interactions with the alignment medium, especially if the analyte molecules are flexible. Considering interactions with alignment media in RDC analysis, we developed and evaluated a molecular docking-based approach to generate more accurate conformer ensembles for compounds in the presence of the poly-γ-benzyl-L-glutamate alignment medium. We designed chiral phosphorus-containing compounds that enabled us to utilize 31P NMR parameters for the stereochemical analysis. Using P3D/PALES software to evaluate diastereomer discrimination, we found that our conformer ensembles outperform moderately the standard, low-energy conformers in RDC analysis. To further improve our results, we (i) averaged the experimental values of the molecular docking-based conformers by applying the Boltzmann distribution and (ii) optimized the structures through normal mode relaxation, thereby enhancing the Pearson correlation factor R and even diastereomer discrimination in some cases. Nevertheless, we presume that significant differences between J-couplings in isotropic and in anisotropic environments may preclude RDC measurements for flexible molecules. Therefore, generating conformer ensembles based on molecular docking enhances RDC analysis for mildly flexible systems while flexible molecules may require applying more advanced approaches, in particular approaches including dynamical effects.

Can Copper(I) and Silver(I) be Hydrogen Bond Acceptors?

Gold(I) centers can form moderately strong (Au⋅⋅⋅H) hydrogen bonds with tertiary ammonium groups, as has been demonstrated in the 3AuCl+ (3+ =1-(tert-butyl)-3-phenyl-4-(2-((dimethylammonio)methyl)phenyl)-1,2,4-triazol-5-ylidene) complex. However, similar hydrogen bonding interactions with isoelectronic silver(I) or copper(I) centers are unknown. Herein, we first explored whether the Au⋅⋅⋅H bond originally observed in 3AuCl+ can be strengthened by replacing Cl with Br or I. Experimental gas-phase IR spectra in the ∼3000 cm-1 region showed only a small effect of the halogen on the Au⋅⋅⋅H bond. Next, we measured the spectra of 3AgCl+ , which exhibited significant differences compared to its 3AuX+ counterparts. The difference has been explained by DFT calculations which indicated that the Ag⋅⋅⋅H interaction is only marginal in this complex, and a Cl⋅⋅⋅H hydrogen bond is formed instead. Calculations predicted the same for the 3CuCl+ complex. However, we noticed that for Ag and Cu complexes with less flexible ligands, such as dimethyl(2-(dimethylammonio)phenyl)phosphine (L7 H+ ), the computations predict the presence of the respective Ag⋅⋅⋅H and Cu⋅⋅⋅H hydrogen bonds, with a strength similar to the Au⋅⋅⋅H bond in 3AuCl+ . We, therefore, propose possible complexes where the presence of (Ag/Cu)⋅⋅⋅H bonds could be experimentally verified to broaden our understanding of these unusual interactions.

Unraveling actinide-actinide bonding in fullerene cages: a DFT versus ab initio methodological study.

Actinide-actinide bonding poses a challenge for both experimental and theoretical chemists because of both the scarcity of experimental data and the exotic nature of actinide bonding due to the involvement and mixing of actinide 7s-, 6p-, 6d-, and particularly 5f-orbitals. Only a few experimental examples of An-An bonding have been reported so far. Here, we perform a methodological study of actinide-actinide bonding on experimentally known Th2@C80 and U2@C80 systems. We compared selected GGA, meta-GGA, hybrid-GGA and range-separated hybrid-GGA functionals with the results obtained using a multireference CASPT2 method, which we consider as a reference point. We show that functionals such as BP86, PBE or TPSS perform well for predicting geometries, while range-separated hybrids are superior in the description of the chemical bonding. None of the tested functionals were deemed reliable regarding the correct electronic spin ground state. Based on the results of this methodological study, we re-evaluate selected previously studied diactinide fullerene systems using more reliable protocol.

The essential role of symmetry in understanding 3He chemical shifts in endohedral helium fullerenes.

The 3He atom is an excellent NMR probe, particularly when enclosed in endohedral helium fullerenes. The 3He chemical shift, δ(3He), in fullerenes spans a range from ca. -50 to +10 ppm, and changes sensitively between different cages, isomers, and external substituents. Reduction of the fullerenes to anions changes the δ(3He) dramatically and unexpectedly, particularly for the most symmetric and also the most abundant C60 and C70 cages. While the 3He atom is shielded by ∼43 ppm upon charging the He@C60 to He@C606-, it is correspondingly deshielded by ∼37 ppm in the He@C70/He@C706- pair. Here, we show that such puzzling differences in δ(3He) relate to the high symmetry of the host fullerene cages. While similar shielding is induced at the 3He atom by the core orbitals of different cages, the symmetry of the cage allows or quenches large paramagnetic, i.e., deshielding orbital interactions of frontier orbitals upon charging of the cage, which is directly responsible for the large observed chemical shift range of endohedral 3He.

A quest for ideal electric field-driven MX@C70 endohedral fullerene memristors: which MX fits the best?

Endohedral fullerenes with a dipolar molecule enclosed in the fullerene cage have great potential in molecular electronics, such as diodes, switches, or molecular memristors. Here, we study a series of model systems based on MX@D5h(1)-C70 (M = a metal or hydrogen, X = a halogen or a chalcogen) endohedral fullerenes to identify potential molecular memristors and to derive a general formula for rapid identification of potential memristors among analogous MX@Cn systems. To obtain sufficiently accurate results for switching barriers and encapsulation energies, we perform a benchmark of ten DFT functionals against ab initio SCS-MP2 and DLPNO-CCSD(T) methods at the complete basis set limit. The whole series is then investigated using the PBE0 functional which was found to be the most efficient vs. the ab initio methods. Nine of the 34 MX@C70 molecules studied are predicted to have suitable switching barriers to be considered as potential candidates for molecular switches and memristors. We have identified several structure-property relationships for the switching barrier and response of the systems to the electric field, in particular the dependence of the switching barrier on the available space for M-X switching and faster response of the system to the electric field with a larger dipole moment of MX and MX@C70.

Cationic Gold(II) Complexes: Experimental and Theoretical Study.

Gold(II) complexes are rare, and their application to the catalysis of chemical transformations is underexplored. The reason is their easy oxidation or reduction to more stable gold(III) or gold(I) complexes, respectively. We explored the thermodynamics of the formation of [AuII (L)(X)]+ complexes (L=ligand, X=halogen) from the corresponding gold(III) precursors and investigated their stability and spectral properties in the IR and visible range in the gas phase. The results show that the best ancillary ligands L for stabilizing gaseous [AuII (L)(X)]+ complexes are bidentate and tridentate ligands with nitrogen donor atoms. The electronic structure and spectral properties of the investigated gold(II) complexes were correlated with quantum chemical calculations. The results show that the molecular and electronic structure of the gold(II) complexes as well as their spectroscopic properties are very similar to those of analogous stable copper(II) complexes.

Comprehensive Theoretical View of the [Cu2 O2 ] Side-on-Peroxo-/Bis-µ-Oxo Equilibria.

Coupled binuclear copper (CBC) sites are employed by many metalloenzymes to catalyze a broad set of biochemical transformations. Typically, the CBC catalytic sites are activated by the O2 molecule to form various [Cu2 O2 ] reactive species. This has also inspired synthesis and development of various biomimetic inorganic complexes featuring the CBC core. From theoretical perspective, the [Cu2 O2 ] reactivity often hinges on the side-on-peroxo-dicopper(II) (P) vs. bis-µ-oxo-dicopper(III) (O) isomerism - an equilibrium that has become almost iconic in theoretical bioinorganic chemistry. Herein, we present a comprehensive calibration and evaluation of the performance of various composite computational protocols available in contemporary computational chemistry, involving coupled-cluster and multireference (relativistic) wave function methods, popular density functionals and solvation models. Starting with the well-studied reference [Cu2 O2 (NH3 )6 ]2+ system, we compared the performance of electronic structure methods and discussed the relativistic effects. This allowed us to select several 'calibrated' DFT functionals that can be conveniently employed to study ten experimentally well-characterized [Cu2 O2 ] inorganic systems. We mostly predicted the lowest-energy structures (P vs. O) of the studied systems correctly. In addition, we present calibration of the used electronic structure methods for prediction of the spectroscopic features of the [Cu2 O2 ] core, mostly provided by the resonance Raman (rR) spectroscopy.

Relativistic Heavy-Neighbor-Atom Effects on NMR Shifts: Concepts and Trends Across the Periodic Table.

Chemical shifts present crucial information about an NMR spectrum. They show the influence of the chemical environment on the nuclei being probed. Relativistic effects caused by the presence of an atom of a heavy element in a compound can appreciably, even drastically, alter the NMR shifts of the nearby nuclei. A fundamental understanding of such relativistic effects on NMR shifts is important in many branches of chemical and physical science. This review provides a comprehensive overview of the tools, concepts, and periodic trends pertaining to the shielding effects by a neighboring heavy atom in diamagnetic systems, with particular emphasis on the "spin-orbit heavy-atom effect on the light-atom" NMR shift (SO-HALA effect). The analyses and tools described in this review provide guidelines to help NMR spectroscopists and computational chemists estimate the ranges of the NMR shifts for an unknown compound, identify intermediates in catalytic and other processes, analyze conformational aspects and intermolecular interactions, and predict trends in series of compounds throughout the Periodic Table. The present review provides a current snapshot of this important subfield of NMR spectroscopy and a basis and framework for including future findings in the field.

On the origin of the inverted singlet-triplet gap of the 5th generation light-emitting molecules.

Excitation energies of the lowest singlet and triplet state of molecules whose first excited singlet state lies energetically below the first triplet state have been studied computationally at (time-dependent) density functional theory, coupled-cluster, and second-order multiconfiguration perturbation theory levels. The calculations at the ab initio levels show that the singlet-triplet gap is inverted as compared to the one expected from Hund's rule, whereas all density functionals yield the triplet state as the lowest excited state. Double excitations responsible for the inverted singlet-triplet gap have been identified. Employing the spin-flip and ΔSCF methods, singlet-triplet inversion was obtained at the density functional theory level for some of the studied molecules.

Experimental and Theoretical Evidence of Spin-Orbit Heavy Atom on the Light Atom 1 H†NMR Chemical Shifts Induced through H⋠⋠⋠I- Hydrogen Bond.

Invited for the cover of this issue is the group of Michal Straka and Martin Dracínský (IOCB Prague, Czech Academy of Sciences). The image depicts a neutron star, which is used to represent the relativistic effects between a heavy element and a hydrogen atom reported in this work. Read the full text of the article at 10.1002/chem.202001532.

Experimental and Theoretical Evidence of Spin-Orbit Heavy Atom on the Light Atom 1 H†NMR Chemical Shifts Induced through H⋠⋠⋠I- Hydrogen Bond.

Spin-orbit (SO) heavy-atom on the light-atom (SO-HALA) effect is the largest relativistic effect caused by a heavy atom on its light-atom neighbors, leading, for example, to unexpected NMR chemical shifts of 1 H, 13 C, and 15 N nuclei. In this study, a combined experimental and theoretical evidence for the SO-HALA effect transmitted through hydrogen bond is presented. Solid-state NMR data for a series of 4-dimethylaminopyridine salts containing I- , Br- and Cl- counter ions were obtained experimentally and by theoretical calculations. A comparison of the experimental chemical shifts with those calculated by a standard DFT methodology without the SO contribution to the chemical shifts revealed a remarkable error of the calculated proton chemical shift of a hydrogen atom that is in close contact with the iodide anion. The addition of the relativistic SO correction in the calculations significantly improves overall agreement with the experiment and confirms the propagation of the SO-HALA effect through hydrogen bonds.

From π Bonds without σ Bonds to the Longest Metal-Metal Bond Ever: A Survey on Actinide-Actinide Bonding in Fullerenes.

Actinide-actinide bonds are rare. Only a few experimental systems with An-An bonds have been described so far. Recent experimental characterization of the U2@Ih(7)-C80 (J. Am. Chem. Soc. 2018, 140, 3907) system with one-electron two-center (OETC) U-U bonds as was predicted by some of us (Phys. Chem. Chem. Phys. 2015, 17, 24182) encourages the search for more examples of actinide-actinide bonding in fullerene cages. Here, we investigate actinide-actinide bonding in An2@D5h(1)-C70, An2@Ih(7)-C80, and An2@D5h(1)-C90 (An = Ac-Cm) endohedral metallofullerenes (EMFs). Using different methods of the chemical bonding analysis, we show that most of the studied An2@C70 and An2@C80 systems feature one or more one-electron two-center actinide-actinide bonds. Unique bonding patterns are revealed in plutonium EMFs. The Pu2@Ih(7)-C80 features two OETC Pu-Pu π bonds without any evidence of a corresponding σ bond. In the Pu2@D5h(1)-C90 with rPu-Pu = 5.9 Å, theory predicts the longest metal-metal bond ever described. Predicted systems are thermodynamically stable and should be, in principle, experimentally accessible, though radioactivity of studied metals may be a serious obstacle.

Fullerene-Based Switching Molecular Diodes Controlled by Oriented External Electric Fields.

Employing multiscale in silico modeling, we propose switching molecular diodes on the basis of endohedral fullerenes (fullerene switching diode, FSD), encapsulated with polar molecules of general type MX (M: metal, X: nonmetal) to be used for data storage and processing. Here, we demonstrate for MX@C70 systems that the relative orientation of enclosed MX with respect to a set of electrodes connected to the system can be controlled by application of oriented external electric field(s). We suggest systems with two- and four-terminal electrodes, in which the source and drain electrodes help the current to pass through the device and help the switching between the conductive states of FSD via applied voltage. The gate electrodes then assist the switching by effectively lowering the energy barrier between local minima via stabilizing the transition state of switching process if the applied voltage between the source and drain is insufficient to switch the MX inside the fullerene. Using nonequilibrium Green's function combined with density functional theory (DFT-NEGF) computations, we further show that conductivity of the studied MX@C70 systems depends on the relative orientation of MX inside the cage with respect to the electrodes. Therefore, the orientation of the MX inside C70 can be both enforced ("written") and retrieved ("read") by applied voltage. The studied systems thus behave like voltage-sensitive switching molecular diodes, which is reminiscent of a molecular memristor.

Spectroscopic and Computational Evidence of Intramolecular AuI ⋠⋠⋠H+ -N Hydrogen Bonding.

Despite substantial evidence of short Au⋅⋅⋅H-X contacts derived from a number of X-ray structures of AuI compounds, the nature of AuI ⋅⋅⋅H bonding in these systems has not been clearly understood. Herein, we present the first spectroscopic evidence for an intramolecular AuI ⋅⋅⋅H+ -N hydrogen bond in a [Cl-Au-L]+ complex, where L is a protonated N-heterocyclic carbene. The complex was isolated in the gas phase and characterized with helium-tagging infrared photodissociation (IRPD) spectra, in which H+ -N-mode-derived bands evidence the intramolecular AuI ⋅⋅⋅H+ -N bond. Quantum chemical calculations reproduce the experimental IRPD spectra and allow to characterize the intramolecular Au⋅⋅⋅H+ -N bonding with a short rAu⋅⋅⋅H distance of 2.17 Šand an interaction energy of approximately -10 kcal mol-1 . Various theoretical descriptors of chemical bonding calculated for the Au⋅⋅⋅H+ -N interaction provide strong evidence for a hydrogen bond of moderate strength.

How Does a Container Affect Acidity of its Content: Charge-Depletion Bonding Inside Fullerenes.

A recent study (Sci. Adv. 2017, 3, e1602833) has shown that FH⋅⋅⋅OH2 hydrogen bond in a HF⋅H2 O pair substantially shortens, and the H-F bond elongates upon encapsulation of the cluster in C70 fullerene. This has been attributed to compression of the HF⋅H2 O pair inside the cavity of C70 . Herein, we present theoretical evidence that the effect is not caused by a mere compression of the H2 O⋅HF pair, but it is related to a strong lone-pair-π (LP-π) bonding with the fullerene cage. To support this argument, a systematic electronic structure study of selected small molecules (HF, H2 O, and NH3 ) and their pairs enclosed in fullerene cages (C60 , C70 , and C90 ) has been performed. Bonding analysis revealed unique LP-πcage interactions with a charge-depletion character in the bonding region, unlike usual LP-π bonds. The LP-πcage interactions were found to be responsible for elongation of the H-F bond. Thus, the HF appears to be more acidic inside the cage. The shortening of the FH⋅⋅⋅OH2 contact in (HF⋅H2 O)@C70 originates from an increased acidity of the HF inside the fullerenes. Such trends were also observed in other studied systems.

Buckyball Difluoride F2 - @C60 + -A Single-Molecule Crystal.

We report the F2 @C60 system as the first example of an endohedral fullerene in which C60 acts as a cation C60 + interacting with endohedral anion, F2 - . Our state-of-the-art computations reveal that in F2 @C60 , despite of the known high electron affinity of C60 , an electron is transferred from C60 to F2 resulting in the F2 - @C60 + system. The F-F bond length in F2 @C60 is substantially longer than in free F2 , which is the result of electron-transfer to the antibonding σu molecular orbital of F2 . Interestingly, although there is a full charge-transfer of one electron between C60 and F2 , only negligible delocalized covalent interactions are found between F2 - and C60 + which is a reminiscent of ionic crystals. Therefore, F2 - @C60 + can be considered as a single-molecule crystal. The other encapsulated halogens in C60 do not show such behavior.

Properties of the Only Thorium Fullerene, Th@C84, Uncovered.

Only a single thorium fullerene, Th@C84, has been reported to date (Akiyama, K.; et al. J. Nucl. Radiochem. Sci. 2002, 3, 151-154). Although the system was characterized by UV-vis and XANES (X-ray absorption near edge structure) spectra, its structure and properties remain unknown. In this work we used the density functional calculations to identify molecular and electronic structure of the Th@C84. Series of molecular structures satisfying the ThC84 stoichiometric formula were studied comprising 24 IPR and 110 non-IPR Th@C84 isomers as well as 9 ThC2@C82 IPR isomers. The lowest energy structure is Th@C84-Cs(10) with the singlet ground state. Its predicted electronic absorption spectra are in agreement with the experimentally observed ones. The bonding between the cage and Th was characterized as polar covalent with Th in formal oxidation state IV. The NMR chemical shifts of Th@C84-Cs(10) were predicted to guide the future experimental efforts in identification of this compound.

High-Frequency 1H NMR Chemical Shifts of SnII and PbII Hydrides Induced by Relativistic Effects: Quest for PbII Hydrides.

The role of relativistic effects on 1H NMR chemical shifts of SnII and PbII hydrides is investigated by using fully relativistic DFT calculations. The stability of possible PbII hydride isomers is studied together with their 1H NMR chemical shifts, which are predicted in the high-frequency region, up to 90 ppm. These 1H signals are dictated by sizable relativistic contributions due to spin-orbit coupling at the heavy atom and can be as large as 80 ppm for a hydrogen atom bound to PbII. Such high-frequency 1H NMR chemical shifts of PbII hydride resonances cannot be detected in the 1H NMR spectra with standard experimental setup. Extended 1H NMR spectral ranges are thus suggested for studies of PbII compounds. Modulation of spin-orbit relativistic contribution to 1H NMR chemical shift is found to be important also in the experimentally known SnII hydrides. Because the 1H NMR chemical shifts were found to be rather sensitive to the changes in the coordination sphere of the central metal in both SnII and PbII hydrides, their application for structural investigation is suggested.

High-Frequency (13)C and (29)Si NMR Chemical Shifts in Diamagnetic Low-Valence Compounds of Tl(I) and Pb(II): Decisive Role of Relativistic Effects.

The (13)C and (29)Si NMR signals of ligand atoms directly bonded to Tl(I) or Pb(II) heavy-element centers are predicted to resonate at very high frequencies, up to 400 ppm for (13)C and over 1000 ppm for (29)Si, outside the typical experimental NMR chemical-shift ranges for a given type of nuclei. The large (13)C and (29)Si NMR chemical shifts are ascribed to sizable relativistic spin-orbit effects, which can amount to more than 200 ppm for (13)C and more than 1000 ppm for (29)Si, values unexpected for diamagnetic compounds of the main group elements. The origin of the vast spin-orbit contributions to the (13)C and (29)Si NMR shifts is traced to the highly efficient 6p → 6p* metal-based orbital magnetic couplings and related to the 6p orbital-based bonding together with the low-energy gaps between the occupied and virtual orbital subspaces in the subvalent Tl(I) and Pb(II) compounds. New NMR spectral regions for these compounds are suggested based on the fully relativistic density functional theory calculations in the Dirac-Coulomb framework carefully calibrated on the experimentally known NMR data for Tl(I) and Pb(II) complexes.