Pseudo-Contact NMR Shifts over the Paramagnetic Metalloprotein CoMMP-12 from First Principles

Delving into theoretical and computational considerations for accurate calculation of chemical shifts in paramagnetic transition metal systems using quantum chemical methods

The chemical shielding tensor for a paramagnetic system has been derived from the macroscopically observed magnetization using the perturbation theory. An approach to calculate the paramagnetic chemical shifts in transition metal systems based on the spin-only magnetic susceptibility directly evaluated from the ab initio Hilbert space of the electronic Zeeman Hamiltonian has been discussed. Computationally, several advantages are associated with this approach: (a) it includes the state-specific paramagnetic Curie (first-order) and Van Vleck (second-order) contributions of the paramagnetic ion to the paramagnetic chemical shifts; (b) thus it avoids the system-specific modeling and evaluating effectively in terms of the electron paramagnetic resonance (EPR) spin Hamiltonian parameters of the magnetic moment of the paramagnetic ion formulated previously; (c) it can be utilized both in the point-dipole (PD) approximation (in the long-range) and with the quantum chemical (QC) method based the hyperfine tensors (in the short-range). Additionally, we have examined the predictive performance of various density functional theory (DFT) functionals of different families and commonly used core-augmented basis sets for nuclear magnetic resonance (NMR) chemical shifts. A selection of transition metal ion complexes with and without first-order orbital contributions, namely the [M(AcPyOx)3(BPh)]+ complexes of M = Mn2+, Ni2+ and Co2+ ions and CoTp2 complex and their reported NMR chemical shifts are studied from QC methods for illustration.

Unravelling the effect of paramagnetic Ni2+ on the 13C NMR shift tensor for carbonate in Mg2-xNixAl layered double hydroxides by quantum-chemical computations

Structural disorder and low crystallinity render it challenging to characterise the atomic-level structure of layered double hydroxides (LDH). We report a novel multi-step, first-principles computational workflow for the analysis of paramagnetic solid-state NMR of complex inorganic systems such as LDH, which are commonly used as catalysts and energy storage materials. A series of 13CO32--labelled Mg2-xNixAl-LDH, x ranging from 0 (Mg2Al-LDH) to 2 (Ni2Al-LDH), features three distinct eigenvalues δ11, δ22 and δ33 of the experimental 13C chemical shift tensor. The δii correlate directly with the concentration of the paramagnetic Ni2+ and span a range of |δ11 - δ33| ≈ 90 ppm at x = 0, increasing to 950 ppm at x = 2. In contrast, the isotropic shift, δiso(13C), only varies by -14 ppm in the series. Detailed insight is obtained by computing (1) the orbital shielding by periodic density-functional theory involving interlayer water, (2) the long-range pseudocontact contribution of the randomly distributed Ni2+ ions in the cation layers (characterised by an ab initio susceptibility tensor) by a lattice sum, and (3) the close-range hyperfine terms using a full first-principles shielding machinery. A pseudohydrogen-terminated two-layer cluster model is used to compute (3), particularly the contact terms. Due to negative spin density contribution at the 13C site arising from the close-by Ni2+ sites, this step is necessary to reach a semiquantitative agreement with experiment. These findings influence future NMR investigations of the formally closed-shell interlayer species within LDH, such as the anions or water. Furthermore, the workflow is applicable to a variety of complex materials.

Electron correlation and vibrational effects in predictions of paramagnetic NMR shifts

Electronic structure calculations are fundamentally important for the interpretation of nuclear magnetic resonance (NMR) spectra from paramagnetic systems that include organometallic and inorganic compounds, catalysts, or metal-binding sites in proteins. Prediction of induced paramagnetic NMR shifts requires knowledge of electron paramagnetic resonance (EPR) parameters: the electronic g tensor, zero-field splitting D tensor, and hyperfine A tensor. The isotropic part of A, called the hyperfine coupling constant (HFCC), is one of the most troublesome properties for quantum chemistry calculations. Yet, even relatively small errors in calculations of HFCC tend to propagate into large errors in the predicted NMR shifts. The poor quality of A tensors that are currently calculated using density functional theory (DFT) constitutes a bottleneck in improving the reliability of interpretation of the NMR spectra from paramagnetic systems. In this work, electron correlation effects in calculations of HFCCs with a hierarchy of ab initio methods were assessed, and the applicability of different levels of DFT approximations and the coupled cluster singles and doubles (CCSD) method was tested. These assessments were performed for the set of selected test systems comprising an organic radical, and complexes with transition metal and rare-earth ions, for which experimental data are available. Severe deficiencies of DFT were revealed but the CCSD method was able to deliver good agreement with experimental data for all systems considered, however, at substantial computational costs. We proposed a more computationally tractable alternative, where the A was computed with the coupled cluster theory exploiting locality of electron correlation. This alternative is based on the domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) method. In this way the robustness and reliability of the coupled cluster theory were incorporated into the modern formalism for the prediction of induced paramagnetic NMR shifts, and became applicable to systems of chemical interest. This approach was verified for the bis(cyclopentadienyl)vanadium(II) complex (Cp₂V; vanadocene), and the metal-binding site of the Zn²⁺ → Co²⁺ substituted superoxide dismutase (SOD) metalloprotein. Excellent agreement with experimental NMR shifts was achieved, which represented a substantial improvement over previous theoretical attempts. The effects of vibrational corrections to orbital shielding and hyperfine tensor were evaluated and discussed within the second-order vibrational perturbation theory (VPT2) framework.

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

Bee venom and its active component Melittin synergistically potentiate the anticancer effect of Sorafenib against HepG2 cells

There are current attempts to find a safe substitute or adjuvant for Sorafenib (Sorf), the standard treatment for advanced hepatocellular carcinoma (HCC), as it triggers very harsh side effects and drug-resistance. The therapeutic properties of Bee Venom (BV) and its active component, Melittin (Mel), make them suitable candidates as potential anti-cancer agents per-se or as adjuvants for cancer chemotherapy. Hence, this study aimed to evaluate the combining effect of BV and Mel with Sorf on HepG2 cells and to investigate their molecular mechanisms of action. Docking between Mel and different tumor-markers was performed. The cytotoxicity of BV, Mel and Sorf on HepG2 and THLE-2 cells was conducted. Combinations of BV/Sorf and Mel/Sorf were performed in non-constant ratios on HepG2. Expression of major cancer-related genes and oxidative stress status was evaluated and the cell cycle was analyzed. The computational analysis showed that Mel can bind to and inhibit XIAP, Bcl2, MDM2, CDK2 and MMP12. Single treatments of BV, Mel and Sorf on HepG2 showed lower IC₅₀than on THLE-2. All combinations revealed a synergistic effect at a combination index (CI) < 1. Significant upregulation (p < 0.05) of p53, Bax, Cas3, Cas7 and PTEN and significant downregulation (p < 0.05) of Bcl-2, Cyclin-D1, Rac1, Nf-κB, HIF-1a, VEGF and MMP9 were observed. The oxidative stress markers including MDA, SOD, CAT and GPx showed insignificant changes, while the cell cycle was arrested at G2/M phase. In conclusion, BV and Mel have a synergistic anticancer effect with Sorf on HepG2 that may represent a new enhancing strategy for HCC treatment.

A High-Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties

Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.

Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase

Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.

How the Ligand Field in Lanthanide Coordination Complexes Determines Magnetic Susceptibility Anisotropy, Paramagnetic NMR Shift, and Relaxation Behavior

Complexes of lanthanide(III) ions are being actively studied because of their unique ground and excited state properties and the associated optical and magnetic behavior. In particular, they are used as emissive probes in optical spectroscopy and microscopy and as contrast agents in magnetic resonance imaging (MRI). However, the design of new complexes with specific optical and magnetic properties requires a thorough understanding of the correlation between molecular structure and electric and magnetic susceptibilities, as well as their anisotropies. The traditional Judd-Ofelt-Mason theory has failed to offer useful guidelines for systematic design of emissive lanthanide optical probes. Similarly, Bleaney's theory of magnetic anisotropy and its modifications fail to provide accurate detail that permits new paramagnetic shift reagents to be designed rather than discovered.A key determinant of optical and magnetic behavior in f-element compounds is the ligand field, often considered as an electrostatic field at the lanthanide created by the ligands. The resulting energy level splitting is a sensitive function of several factors: the nature and polarizability of the whole ligand and its donor atoms; the geometric details of the coordination polyhedron; the presence and extent of solvent interactions; specific hydrogen bonding effects on donor atoms and the degree of supramolecular order in the system. The relative importance of these factors can vary widely for different lanthanide ions and ligands. For nuclear magnetic properties, it is both the ligand field splitting and the magnetic susceptibility tensor, notably its anisotropy, that determine paramagnetic shifts and nuclear relaxation enhancement.We review the factors that control the ligand field in lanthanide complexes and link these to aspects of their utility in magnetic resonance and optical emission spectroscopy and imaging. We examine recent progress in this area particularly in the theory of paramagnetic chemical shift and relaxation enhancement, where some long-neglected effects of zero-field splitting, magnetic susceptibility anisotropy, and spatial distribution of lanthanide tags have been accommodated in an elegant way.