On the importance of anion-π interactions in the mechanism of sulfide:quinone oxidoreductase

Structure-directing role of CH⋯X (X = C, N, S, Cl) interactions in three ionic cobalt complexes: X-ray investigation and DFT study using QTAIM Vr predictor to eliminate the effect of pure Coulombic forces

Three cobalt complexes, namely [CoIII(HL1)2(N3)2]ClO4 (1), [CoIII(L2)(HL2)(N3)]ClO4·1.5H2O (2), and [CoIII(L3)(HL3)(NCS)]2 [CoIICl2(NCS)2] (3), where HL1 = 2-(3-(dimethylamino)propyliminomethyl)-6-methoxyphenol, HL2 = 2-(2-(dimethylamino)ethyliminomethyl)-4,6-dichlorophenol, and HL3 = 2-(2-(dimethylamino)ethyliminomethyl)-6-methoxyphenol, as potential tridentate N2O-donor Schiff base ligands, were synthesized and characterized using elemental analysis, IR and UV-vis spectroscopy, and single-crystal X-ray diffraction studies. All three were found to be monomeric ionic complexes. Complex 1 crystallizes in the orthorhombic space group Pbcn, whereas both complexes 2 and 3 crystallize in triclinic space groups, P1̄. Further, 1 and 2 are cationic complexes of octahedral cobalt(iii) with perchlorate anions, whereas complex 3 contains a cationic part of octahedral cobalt(iii) and an anionic part of tetrahedral cobalt(ii). Hydrogen-bonding interactions involving aromatic and aliphatic CH bonds as H-bond donors and the pseudo-halide co-ligands as H-bond acceptors were established, which are important aspects governing the X-ray packing. These interactions were analyzed theoretically using the quantum theory of atoms in molecules (QTAIM) and non-covalent interaction plot (NCI plot) analyses. Moreover, energy decomposition analysis (EDA) was performed to analyze the stabilization of the complexes in terms of the electrostatic, dispersion, and correlation forces.

Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules

We present a systematic structural and energetic characterization of phosphate(OP)-nucleobase anion…π stacking interactions in RNAs. We observed OP-nucleobase stacking contacts in a variety of structural motifs other than regular helices and spanning broadly diverse sequence distances. Apart from the stacking between a phosphate and a guanine or a uracil two-residue upstream in specific U-turns, such interactions in RNA have been scarcely characterized to date. Our QM calculations showed an energy minimum at a distance between the OP atom and the nucleobase plane centroid slightly below 3 Å for all the nucleobases. By sliding the OP atom over the nucleobase plane we localized the optimal mutual positioning of the stacked moieties, corresponding to an energy minimum below -6 kcal•mol-1, for all the nucleobases, consistently with the projections of the OP atoms over the different π-rings we observed in experimental occurrences. We also found that the strength of the interaction clearly correlates with its electrostatic component, pointing to it as the most relevant contribution. Finally, as OP-uracil and OP-guanine interactions represent together 86% of the instances we detected, we also proved their stability under dynamic conditions in model systems simulated by state-of-the art DFT-MD calculations.

Quinone binding site in a type VI sulfide:quinone oxidoreductase

Monotopic membrane-bound flavoproteins, sulfide:quinone oxidoreductases (SQRs), have a variety of physiological functions, including sulfide detoxification. SQR enzymes are classified into six groups. SQRs use the flavin adenine dinucleotide (FAD) cofactor to transfer electrons from sulfide to quinone. A type VI SQR of the photosynthetic purple sulfur bacterium, Thiocapsa roseopersicina (TrSqrF), has been previously characterized, and the mechanism of sulfide oxidation has been proposed. This paper reports the characterization of quinone binding site (QBS) of TrSqrF composed of conserved aromatic and apolar amino acids. Val331, Ile333, and Phe366 were identified near the benzoquinone ring of enzyme-bound decylubiquinone (dUQ) using the TrSqrF homology model. In silico analysis revealed that Val331 and Ile333 alternately connected with the quinone head group via hydrogen bonds, and Phe366 and Trp369 bound the quinones via hydrophobic interactions. TrSqrF variants containing alanine (V331A, I333A, F366A) and aromatic amino acid (V331F, I333F, F366Y), as well as a C-terminal α-helix deletion (CTD) mutant were generated. These amino acids are critical for quinone binding and, thus, catalysis. Spectroscopic analyses proved that all mutants contained FAD. I333F replacement resulted in the lack of the charge transfer complex. In summary, the interactions described above maintain the quinone molecule's head in an optimal position for direct electron transfer from FAD. Surprisingly, the CTD mutant retained a relatively high level of specific activity while remaining membrane-anchored. This is a unique study because it focuses on the QBS and the oxidative stage of a type VI sulfide-dependent quinone reduction. KEY POINTS: • V331, I333, F366, and W369 were shown to interact with decylubiquinone in T. roseopersicina SqrF • These amino acids are involved in proper positioning of quinones next to FAD • I333 is essential in formation of a charge transfer complex from FAD to quinone.

Benzene, an Unexpected Binding Unit in Anion–π Recognition: The Critical Role of CH/π Interactions

We report high-level ab initio calculations (CCSD(T)(full)/CBS//SCS-RI-MP2(full)/aug-cc-pwCVTZ) that demonstrate the importance of cooperativity effects when Anion–π and CH/π interactions are simultaneously established with benzene as the π-system. In fact, most of the complexes exhibit high cooperativity energies that range from 17% to 25.3% of the total interaction energy, which is indicative of the strong influence of the CH/π on the Anion–π interaction and vice versa. Moreover, the symmetry-adapted perturbation theory (SAPT) partition scheme was used to study the different energy contributions to the interaction energies and to investigate the physical nature of the interplay between both interactions. Furthermore, the Atoms in Molecules (AIM) theory and the Non-Covalent Interaction (NCI) approach were used to analyze the two interactions further. Finally, a few examples from the Protein Data Bank (PDB) are shown. All results stress that the concurrent formation of both interactions may play an important role in biological systems due to the ubiquity of CH bonds, phenyl rings, and anions in biomolecules.

Mining anion-aromatic interactions in the Protein Data Bank

Mutual positioning and non-covalent interactions in anion–aromatic motifs are crucial for functional performance of biological systems. In this context, regular, comprehensive Protein Data Bank (PDB) screening that involves various scientific points of view and individual critical analysis is of utmost importance. Analysis of anions in spheres with radii of 5 Å around all 5- and 6-membered aromatic rings allowed us to distinguish 555 259 unique anion–aromatic motifs, including 92 660 structures out of the 171 588 structural files in the PDB. The use of a scarcely exploited (x, h) coordinate system led to (i) identification of three separate areas of motif accumulation: A – over the ring, B – over the ring-substituent bonds, and C – roughly in the plane of the aromatic ring, and (ii) unprecedented simultaneous comparative description of various anion–aromatic motifs located in these areas. Of the various residues considered, i.e. aminoacids, nucleotides, and ligands, the latter two exhibited a considerable tendency to locate in region Avia archetypal anion–π contacts. The applied model not only enabled statistical quantitative analysis of space around the ring, but also enabled discussion of local intermolecular arrangements, as well as detailed sequence and secondary structure analysis, e.g. anion–π interactions in the GNRA tetraloop in RNA and protein helical structures. As a purely practical issue of this work, the new code source for the PDB research was produced, tested and made freely available at https://github.com/chemiczny/PDB_supramolecular_search.

The comprehensive analysis of non-redundant PDB macromolecular structures investigating anion distributions around all aromatic molecules in available biosystems is presented.

Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study

In this study, we demonstrate that anion−π interactions (an attractive noncovalent force between electron deficient π-systems and anions) are involved in the stabilization of GAAA and GGAG RNA tetraloops. Using the single recognition particle (SRP)–RNA complexes as a case of study, we combined molecular dynamics (MD) and quantum mechanics (QM) calculations to shed light on the structural influence of phosphate–G anion−π interactions and hydrogen bonds (HBs) involving K⁺/Mg²⁺ water clusters. In addition, the RNA assemblies herein were further characterized by means of the “atoms in molecules” (AIM) and noncovalent interactions plot (NCIplot) methodologies. We believe the results derived from this study might be important in the fields of chemical biology (RNA folding and engineering) and supramolecular chemistry (anion−π interactions) as well as to further expand the current knowledge regarding RNA structural motifs.

Exploring the structure-property schemes in anion-π systems of d-block metalates

Anion-π based compounds, materials, and processes have gained significant interest due to the diversity of their aesthetic non-covalent synthons, and thanks to their significance in biological systems, catalytic processes, anion binding and sensing, or the supramolecular organization of hierarchical architectures. While systems based on typical inorganic anions or organic residues have been widely reviewed in recent years, those involving anionic d metal comlexes as the main components have been treated with a rather secondary interest. However, actively exploring the new systems of the latter type we have recognized systematic advances in the field. As a result, in the current review we describe the landscape that has recently emerged. Focusing on the established groups of π-acidic species, i.e. polycarbonitirles, polyazines, polyazine N-oxides, diimide derivatives, fluoroarenes, and nitroarenes, we explore and discuss anion-π crystal engineering together with the structure-property schemes important from the standpoint of charge transfer (CT) and electron transfer (ET), magnetism, luminescence, reactivity and catalysis, and the construction of core-shell crystalline composites.

Binding of anionic Pt(ii) complexes in a dedicated organic matrix: towards new binary crystalline composites

Square-planar [PtL₄]²⁻ (L = CN⁻, Cl⁻, Br⁻) anions are bound by π-acidic HAT(CN)₆ in solution and in the solid state to provide the basis for the first epitaxially grown anion–π crystalline composites.

An insight into the non-covalent Pb⋯S and S⋯S interactions in the solid-state structure of a hemidirected lead(ii) complex

A hemi-directed copper(ii)/lead(ii) complex has been synthesized and characterized. The energy of chalcogen–chalcogen and tetrel bonding interactions in this complex was analyzed by DFT calculations.

Understanding the mechanism of H2S oxidation by flavin-dependent sulfide oxidases: a DFT/IEF-PCM study

In the last years, H₂S has been recognized as a signaling molecule in mammals, which can synthesize and catabolize (by oxidation) such species. The latter process is accelerated by a sulfide:quinone oxidoreductase (SQR, E.C. 1.8.5.4), a flavin-dependent sulfide oxidase (FDSO). FDSOs catalyze electron transfer from H₂S to an acceptor in catalytic cycles involving two phases: (I) reduction of FAD by H₂S (SH^-) and (II) electron transfer from FADH^- to the electron acceptor. The first step of FAD reduction consists on the reaction of SH^- with a catalytic disulfide at the active site of the enzyme, to yield a thiolate and a persulfide in the protein. This step is ca. 10⁶ times faster than the analogous reaction with low-molecular-weight disulfides (LMWDs) and the causes of such extraordinary acceleration remain unknown. Using the IEF-PCM(ε ≈ 10)/M06-2X-D3/6-31+G(d,p) level of theory, we have modeled the reaction of SH^- with a disulfide as located in a representative model of the active site extracted from a prokaryotic SQR, assessing the effects of partial covalent interactions (PCIs) between the leaving sulfur atom and flavin ring on the activation Gibbs free-energy barrier at 298 K (∆^‡G_298K). To also evaluate the importance of entropic penalties on the first step, we have modeled at the same level of theory the reaction of (bis)hydroxyethyl disulfide in aqueous solution, a LMWD for which experimental data is available. Our results show that PCIs between the leaving sulfur atom and the flavin group only have a minor effect (∆^‡G_298K reduced by 1.6 kcal mol^-1) while compensating entropic penalties could have a much larger effect (up to 8.3 kcal mol^-1). Finally, we also present here a first model of some of further steps in the phase I of the catalytic cycle as in mammalian FDSOs, providing some light about their detailed mechanism. Graphical abstract .

Quinone-thioether metabolites of hydroquinone play a dual role in promoting a vicious cycle of ROS generation: in vitro and in silico insights

Humans are exposed to hydroquinone (HQ) via diet, smoking, occupation, and even via inhalation of polluted air. Given its preferential distribution in kidney and liver, the impact of biotransformation on the nephrotoxicity and hepatotoxicity of HQ was evaluated. Indeed, HQ and its metabolites, benzoquinone, and quinone-thioethers (50, 100, 200, and 400 μM) all induced ROS-dependent cell death in both HK-2, a human kidney proximal epithelial cell line, and THLE-2, a human liver epithelial cell line, in a concentration-dependent manner. For a deeper insight into the biological mechanism of ROS stimulation, the bioinformatics database was reviewed. Intriguingly, 163 proteins were currently reported to form co-crystal complex with benzoquinone analogs, a large proportion of which are closely related to ROS generation. After a thorough assessment of the interaction affinity and binding energy, three key mitochondrial proteins that are particularly involved in electric transport, namely, cytochrome BC1, succinate dehydrogenase, and sulfide:quinone oxidoreductase, were highlighted for further verification. Their binding affinity and the action pattern were explored and validated by molecular docking and molecular dynamics simulations. Remarkably, quinone-thioether metabolites of HQ afforded high affinity to the above proteins that purportedly cause a surge in the generation of ROS. Therefore, HQ can be further converted into quinone-thioethers, which on one hand can function as substrates for redox cycling, and on the other hand may afford high affinity with key proteins evolved in mitochondrial electron transport system, leading to a vicious cycle of ROS generation. The combined data provide a prospective insight into the mechanisms of ROS motivation, expanding HQ-mediated toxicology profiles.

Formation of a tetranuclear supramolecule via non-covalent Pb⋯Cl tetrel bonding interaction in a hemidirected lead(ii) complex with a nickel(ii) containing metaloligand

A hetero-nuclear nickel(ii)/lead(ii) complex has been synthesized and characterized. The tetrel bonding interactions established between the σ-hole at the hemi-coordinated lead(ii) and the electron rich chlorido ligand has been analyzed by DFT study.

A combined experimental and computational study on supramolecular assemblies in hetero-tetranuclear nickel(ii)-cadmium(ii) complexes with N2O4-donor compartmental Schiff bases

Two new hetero-tetranuclear nickel(ii)/cadmium(ii) complexes, a cubane [(CH₃CO₂)₂Ni₂(L¹)₂Cd₂(NCS)₂] (1) and a linear tetramer [(DMSO)₂NiL²Cd(NCS)(μ_1,3-SCN)Ni(DMSO)L²Cd(NCS)₂] (2) {where H₂L¹ = N,N'-bis(3-methoxysalicylidene)propane-1,3-diamine and H₂L² = N,N'-bis(3-ethoxysalicylidene)propane-1,3-diamine are potential octadentate compartmental Schiff bases}, were synthesized and characterized. The structures of both complexes were confirmed by single crystal X-ray diffraction studies. Complex 1 contained a Ni₂Cd₂O₄ cubane core, whereas complex 2 featured an end-to-end thiocyanate-bridged tetranuclear moiety. Furthermore, complex 1 showed C-HH-C interactions, whereas a unique Sπ interaction was observed in complex 2. Theoretical studies were performed using several computational tools such as NBO and AIM analyses. Both complexes showed photoluminescence in DMSO medium at room temperature upon irradiation with ultraviolet light. The lifetimes of the excited states were ∼27 ns.

An Anion-π Interaction Strongly Stabilizes the β-Sheet Protein WW

Anions have long been known to engage in stabilizing interactions with electron-deficient arenes. However, the precise nature and energetic contribution of anion-π interactions to protein stability remains a subject of debate. Here, we show that placing a negatively charged Asp in close proximity to electron-rich Phe in a reverse turn within the WW domain results in a favorable interaction that increases WW conformational stability by -1.3 kcal/mol.

Lone pair-π interactions in biological systems: occurrence, function, and physical origin

Lone pair-π interactions are now recognized as a supramolecular bond whose existence in biological systems is documented by a growing number of examples. They are commonly attributed to electrostatic forces. This review attempts to highlight some recent discoveries evidencing the important role which lone pair-π interactions, and anion-π interactions in particular, play in stabilizing the structure and affecting the function of biomolecules. Special attention is paid to studies exploring the physical origin of these at first glance counterintuitive interactions between a lone pair of electrons of one residue and the π-cloud of another. Recent theoretical work went beyond the popular electrostatic model and inquired the extent to which orbital interactions have to be taken into account. In at least one biologically relevant case-that of anion-flavin interactions-a substantial charge-transfer component has been shown to operate.

Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-site Cysteine Persulfide

Very recent studies indicate that sulfur atoms with oxidation state 0 or −1, called sulfane sulfurs, are the actual mediators of some physiological processes previously considered to be regulated by hydrogen sulfide (H₂S). 3-Mercaptopyruvate sulfurtransferase (3MST), one of three H₂S-producing enzymes, was also recently shown to produce sulfane sulfur (H₂S_n). Here, we report the discovery of several potent 3MST inhibitors by means of high-throughput screening (HTS) of a large chemical library (174,118 compounds) with our H₂S-selective fluorescent probe, HSip-1. Most of the identified inhibitors had similar aromatic ring-carbonyl-S-pyrimidone structures. Among them, compound 3 showed very high selectivity for 3MST over other H₂S/sulfane sulfur-producing enzymes and rhodanese. The X-ray crystal structures of 3MST complexes with two of the inhibitors revealed that their target is a persulfurated cysteine residue located in the active site of 3MST. Precise theoretical calculations indicated the presence of a strong long-range electrostatic interaction between the persulfur anion of the persulfurated cysteine residue and the positively charged carbonyl carbon of the pyrimidone moiety of the inhibitor. Our results also provide the experimental support for the idea that the 3MST-catalyzed reaction with 3-mercaptopyruvate proceeds via a ping-pong mechanism.

Experimental investigation of anion–π interactions – applications and biochemical relevance

Anion–π interactions, intuitively repulsive forces, turned from controversial to a well-established non-covalent interaction over the past quarter of a century.

A thorough anion-π interaction study in biomolecules: on the importance of cooperativity effects

The importance of anion–π interactions in key biological processes is reported from a PDB analysis of anion–π interactions in biomolecules, also considering cooperativity effects by including other interactions.

Noncovalent interactions have a constitutive role in the science of intermolecular relationships, particularly those involving aromatic rings such as π–π and cation–π. In recent years, anion–π contact has also been recognized as a noncovalent bonding interaction with important implications in chemical processes. Yet, its involvement in biological processes has been scarcely reported. Herein we present a large-scale PDB analysis of the occurrence of anion–π interactions in proteins and nucleic acids. In addition we have gone a step further by considering the existence of cooperativity effects through the inclusion of a second noncovalent interaction, i.e. π-stacking, T-shaped, or cation–π interactions to form anion–π–π and anion–π–cation triads. The statistical analysis of the thousands of identified interactions reveals striking selectivities and subtle cooperativity effects among the anions, π-systems, and cations in a biological context. The reported results stress the importance of anion–π interactions and the cooperativity that arises from ternary contacts in key biological processes, such as protein folding and function and nucleic acids–protein and protein–protein recognition. We include examples of anion–π interactions and triads putatively involved in enzymatic catalysis, epigenetic gene regulation, antigen–antibody recognition, and protein dimerization.

On the non-classical contribution in lone-pair–π interaction: IQA perspective

Most and least electrostatic repulsive parts of a complex presented by red and blue isosurface repulsive potential energy density.

A combined experimental and computational study of supramolecular assemblies in ternary copper(ii) complexes with a tetradentate N4donor Schiff base and halides

Three new copper(ii) Schiff base complexes have been prepared and characterized. DFT calculations were employed to estimate the contribution of different non-covalent interactions in the extended supra-molecular networks.