NMR chemical shift of confined 129Xe: coordination number, paramagnetic channels and molecular dynamics in a cryptophane-A biosensor

Advances in hyperpolarisation and indirect detection have enabled the development of xenon nuclear magnetic resonance (NMR) biosensors (XBSs) for molecule-selective sensing in down to picomolar concentration. Cryptophanes (Crs) are popular cages for hosting the Xe "spy". Understanding the microscopic host-guest chemistry has remained a challenge in the XBS field. While early NMR computations of XBSs did not consider the important effects of host dynamics and explicit solvent, here we model the motionally averaged, relativistic NMR chemical shift (CS) of free Xe, Xe in a prototypic CrA cage and Xe in a water-soluble CrA derivative, each in an explicit H2O solvent, over system configurations generated at three different levels of molecular dynamics (MD) simulations. We confirm the "contact-type" character of the Xe CS, arising from the increased availability of paramagnetic channels, magnetic couplings between occupied and virtual orbitals through the short-ranged orbital hyperfine operator, when neighbouring atoms are in contact with Xe. Remarkably, the Xe CS in the present, highly dynamic and conformationally flexible situations is found to depend linearly on the coordination number of the Xe atom. We interpret the high- and low-CS situations in terms of the magnetic absorption spectrum and choose our preference among the used MD methods based on comparison with the experimental CS. We check the role of spin-orbit coupling by comparing with fully relativistic CS calculations. The study outlines the computational workflow required to realistically model the CS of Xe confined in dynamic cavity structures under experimental conditions, and contributes to microscopic understanding of XBSs.

The LRESC-Loc Model to Analyze Magnetic Shieldings with Localized Molecular Orbitals

The leading electronic mechanisms of relativistic effects in the NMR magnetic shieldings of heavy-atom (HA) containing molecules are well described by the linear response with elimination of small components model (LRESC). We show here first results from a new version of the LRESC model written in terms of localized molecular orbitals (LMOs) which is coined as LRESC-Loc. Those LMOs resemble "chemist's orbitals", representing lone-pairs, atomic cores, and bonds. The whole set of relativistic effects are expressed in terms of non-ligand-dependent and ligand-dependent contributions. We show the electronic origin of trends and behavior of different mechanisms in molecular systems which contain heavy elements that belong to any of the IB to VIIA groups of the periodic table. The SO mechanism has a well-defined dependence with the LPs (LPσ and LPπ) when the HAs have them, but the non-SO mechanisms mostly depend on other LMOs. In addition we propose here that the SO mechanism can be used to characterize interactions involving LPs and the non-SO mechanisms to characterize covalent and close-shell interactions. All our main results are in accord with previous findings, though we are now able to analyze them in a different manner.

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H₃PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching ~20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules.

Hyper-CEST NMR of metal organic polyhedral cages reveals hidden diastereomers with diverse guest exchange kinetics

Guest capture and release are important properties of self-assembling nanostructures. Over time, a significant fraction of guests might engage in short-lived states with different symmetry and stereoselectivity and transit frequently between multiple environments, thereby escaping common spectroscopy techniques. Here, we investigate the cavity of an iron-based metal organic polyhedron (Fe-MOP) using spin-hyperpolarized ¹²⁹Xe Chemical Exchange Saturation Transfer (hyper-CEST) NMR. We report strong signals unknown from previous studies that persist under different perturbations. On-the-fly delivery of hyperpolarized gas yields CEST signatures that reflect different Xe exchange kinetics from multiple environments. Dilute pools with ~ 10⁴-fold lower spin numbers than reported for directly detected hyperpolarized nuclei are readily detected due to efficient guest turnover. The system is further probed by instantaneous and medium timescale perturbations. Computational modeling indicates that these signals originate likely from Xe bound to three Fe-MOP diastereomers (T, C₃, S₄). The symmetry thus induces steric effects with aperture size changes that tunes selective spin manipulation as it is employed in CEST MRI agents and, potentially, impacts other processes occurring on the millisecond time scale.

XNgNSi (X = HCC, F; Ng = Kr, Xe, Rn): A New Class of Metastable Insertion Compounds Containing Ng-C/F and Ng-N Bonds and Possible Isomerization therein

Recently, astronomically important silaisocyanoacetylene (HCCNSi) possessing a large dipole moment has been detected for the first time with the help of crossed molecular beam experiments. Quantum chemical computations at higher levels of theory have also been performed to characterize the transient species. In this study, we have analyzed the equilibrium geometry, stability, reactivity, and energetics as well as the nature of bonding in the noble gas (Ng) inserted HCCNSi compound. We have also considered its F analogue to understand the influence of the most electronegative atom in the compound. Metastable behavior of the XNgNSi compounds (X = HCC, F; Ng = Kr-Rn) is examined by calculating thermochemical parameters like free energy change (ΔG) and zero-point-energy-corrected dissociation energy (D₀) at 298 K for all possible two-body (2B) and three-body (3B) (both neutral as well as ionic) dissociation channels using coupled-cluster theory [CCSD(T)] in addition to density functional theory (DFT) as well as second order Møller-Plesset perturbation theory (MP2). The set of predicted compounds is found to be endergonic in nature, having high positive free energy change suggesting the thermochemical stability of the compounds except for the 2B Ng-release paths. Though thermodynamically feasible, they are kinetically protected with very high activation free energy barriers. Interestingly, the release of Ng from the parent moiety XNgNSi produces the XSiN isomer, by 180° flipping of the NSi moiety. This can also be seen in the dynamical simulation carried out with the help of atom-centered density matrix propagation (ADMP) technique at 2000K for 1 ps. The bonding in Ng-C, Ng-F, and Ng-N bonds of the studied compounds is analyzed and described with the aid of natural bond orbital (NBO), topological parameters computed using atoms-in-molecules theory (AIM), energy decomposition analysis (EDA), and adaptive natural density partitioning (AdNDP) methods. The natural charge distribution on the constituent atoms suggests that the compounds can be partitioned into both ways of representations, viz., neutral radical as well as ionic fragments. Lastly, the reactivity of the compounds is scrutinized using certain reactivity descriptors calculated within the domain of conceptual density functional theory (CDFT).

On the heavy atom on light atom relativistic effect in the NMR shielding constants of phosphine tellurides

The relativistic HALA effect has been shown to depend on the spatial deformation of the lone electron pairs of a heavy atom, as demonstrated for alkyl and alkene phosphine tellurides. It was found that HALA effect on phosphorous nuclear magnetic resonance shielding constant is strongly dependent on the spatial arrangements of light substituents on phosphorus, resulting in the deformation of the lone electron pairs of tellurium.

An ab initio study on noble gas inserted halogenated acetylene: HNgCCX (Ng = Kr and Xe; X = halogen)

Although HNgCCX (Ng = Kr and Xe; X = F and Cl) have been identified in cryogenic matrices, similar Br and I analogues have not been prepared so far. In this paper, the nature of HNgCCX (Ng = Kr and Xe; X = F, Cl, Br and I) have been investigated by ab initio methods. The main characteristic absorption peak of HNgCCX is the v_H-Ng, which decreases as X varies from F to I. Moreover, the H-Xe bond is stronger than the H-Kr bond. The v_C≡C and v_C-X exhibit red- and blue-shift characters, respectively, especially the C-X bond is abnormal blue-shift halogen bond. AIM results show that the H-Ng bond is essentially covalent bond and the covalent character of H-Xe bond is underestimated, and the trend of the covalent character is C-Cl > C-Br > C-F > C-I. Although HNgCCX is instable thermodynamically with respect to Ng + HCCX, it is kinetically stable with respect to the two-/three-body channels due to the relatively larger energy barriers. The three-body channels of HNgCCX is the main decomposition channel, and the kinetically stability of HXeCCX is more than its Kr analogues. This study is helpful for the preparation of new HNgCCX in cryogenic matrices.

Inside information on xenon adsorption in porous organic cages by NMR

A solid porous molecular crystal formed from an organic cage, CC3, has unprecedented performance for the separation of rare gases. Here, xenon was used as an internal reporter providing extraordinarily versatile information about the gas adsorption phenomena in the cage and window cavities of the material. 129Xe NMR measurements combined with state-of-the-art quantum chemical calculations allowed the determination of the occupancies of the cavities, binding constants, thermodynamic parameters as well as the exchange rates of Xe between the cavities. Chemical exchange saturation transfer (CEST) experiments revealed a minor window cavity site with a significantly lower exchange rate than other sites. Diffusion measurements showed significantly reduced mobility of xenon with loading. 129Xe spectra also revealed that the cage cavity sites are preferred at lower loading levels, due to more favourable binding, whereas window sites come to dominate closer to saturation because of their greater prevalence.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129 Xe NMR Spectroscopy

An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by ¹²⁹ Xe NMR spectroscopy. The high sensitivity of the ¹²⁹ Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

DFT calculations in the assignment of solid-state NMR and crystal structure elucidation of a lanthanum(iii) complex with dithiocarbamate and phenanthroline

Structure of a novel rare-earth lanthanum(iii) complex resolved by a combination of DFT modelling, NMR spectroscopy, and single crystal XRD.

Encapsulation of xenon by a self-assembled Fe4L6 metallosupramolecular cage

We report (129)Xe NMR experiments showing that a Fe4L6 metallosupramolecular cage can encapsulate xenon in water with a binding constant of 16 M(-1). The observations pave the way for exploiting metallosupramolecular cages as economical means to extract rare gases as well as (129)Xe NMR-based bio-, pH, and temperature sensors. Xe in the Fe4L6 cage has an unusual chemical shift downfield from free Xe in water. The exchange rate between the encapsulated and free Xe was determined to be about 10 Hz, potentially allowing signal amplification via chemical exchange saturation transfer. Computational treatment showed that dynamical effects of Xe motion as well as relativistic effects have significant contributions to the chemical shift of Xe in the cage and enabled the replication of the observed linear temperature dependence of the shift.