Prediction of the pKa's of aqueous metal ion +2 complexes

Promoting Oxygen Evolution Electrocatalysis by Coordination Engineering in Cobalt Phosphate

Understanding the structure-activity correlation is an important prerequisite for the rational design of high-efficiency electrocatalysts at the atomic level. However, the effect of coordination environment on electrocatalytic oxygen evolution reaction (OER) remains enigmatic. In this work, the regulation of proton transfer involved in water oxidation by coordination engineering based on Co3(PO4)2 and CoHPO4 is reported. The HPO4 2- anion has intermediate pKa value between Co(II)-H2O and Co(III)-H2O to be served as an appealing proton-coupled electron transfer (PCET) induction group. From theoretical calculations, the pH-dependent OER properties, deuterium kinetic isotope effects, operando electrochemical impedance spectroscopy (EIS) and Raman studies, the CoHPO4 catalyst beneficially reduces the energy barrier of proton hopping and modulates the formation energy of high-valent Co species, thereby enhancing OER activity. This work demonstrates a promising strategy that involves tuning the local coordination environment to optimize PCET steps and electrocatalytic activities for electrochemical applications. In addition, the designed system offers a motif to understand the structure-efficiency relationship from those amino-acid residue with proton buffer ability in natural photosynthesis.

Installing Quinol Proton/Electron Mediators onto Non-Heme Iron Complexes Enables Them to Electrocatalytically Reduce O2 to H2O at High Rates and Low Overpotentials

We prepare iron(II) and iron(III) complexes with polydentate ligands that contain quinols, which can act as electron proton transfer mediators. Although the iron(II) complex with N-(2,5-dihydroxybenzyl)-N,N',N'-tris(2-pyridinylmethyl)-1,2-ethanediamine (H2qp1) is inactive as an electrocatalyst, iron complexes with N,N'-bis(2,5-dihydroxybenzyl)-N,N'-bis(2-pyridinylmethyl)-1,2-ethanediamine (H4qp2) and N-(2,5-dihydroxybenzyl)-N,N'-bis(2-pyridinylmethyl)-1,2-ethanediamine (H2qp3) were found to be much more active and more selective for water production than a previously reported cobalt-H2qp1 electrocatalyst while operating at low overpotentials. The catalysts with H2qp3 can enter the catalytic cycle as either Fe(II) or Fe(III) species; entering the cycle through Fe(III) lowers the effective overpotential. On the basis of their TOF0 values, the successful iron-quinol complexes are better electrocatalysts for oxygen reduction than previously reported iron-porphyrin compounds, with the Fe(III)-H2qp3 arguably being the best homogeneous electrocatalyst for this reaction. With iron, the quinol-for-phenol substitution shifts the product selectivity from H2O2 to water with little impact on the overpotential, but unlike cobalt, this substitution also greatly improves the activity, as assessed by TOFmax, by hastening the protonation and oxygen binding steps. The addition of a second quinol further enhances the activity and selectivity for water but modestly increases the effective overpotential.

Prediction of the pKa's of Hydrated Metal Carbonates and Bicarbonates for Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn Dications

The gas- and aqueous-phase acidities of hydrated metal dication carbonates, bicarbonates, and hydroxide complexes M(CO3)(H2O)n for n = 1 to 3, M(HCO3)2, M(HCO3)2(H2O)2, M(HCO3)(OH), and M(HCO3)(H2O)2(OH) for M = Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn were calculated at the CCSD(T)/aug-cc-pwCVDZ/cc-pwCVDZ level in the gas phase and at the B3LYP/aug-cc-pVTZ/cc-pVTZ(-PP) level with the COSMO self-consistent reaction field (SCRF) method in the aqueous phase. The composite correlated molecular orbital theory G3(MP2) and G3(MP2)B3 methods were used to predict the pKa's of the Mg structures and cis-cis carbonic acid to provide additional benchmarks. Using values scaled to experiment for H2CO3, the pKa's of bicarbonate ligands in group 2 and transition-metal complexes were compared to carbonic acid to gauge the effect of the metal complex on the bicarbonate. The group 2 metal complexes M(HCO3)2 and M(HCO3)(OH) decreased the acidity of the bicarbonate ligands, whereas their dihydrates were even less acidic. The transition-metal di-bicarbonate and bicarbonate hydroxide complexes generally made the bicarbonate more acidic especially when reduction of the metal occurs consistent with electron donation from the ligands; this is accompanied by spin transfer which typically increases in the order Mn < Fe < Co < Ni < Cu. The transition-metal dihydrates were less acidic than carbonic acid. Using values scaled to experiment for hydrated metal dications, the pKa's of water coordinated to group 2 and transition-metal complexes were generally more acidic than the hydrated metal dications, with the exception of Ca bicarbonate dihydrate, Co carbonate, Ni di-bicarbonate dihydrate, and Cu bicarbonate hydroxide di-bicarbonate.

Towards a low-emission resource circulation of valuable metals from municipal solid waste incineration fly ash

The incineration fly ash (IFA) resulting from municipal solid waste combustion is laden with heavy metals, necessitating proper treatment not only for environmental management but also to reclaim the metal values. The surge in non-traditional metals like cobalt as emerging contaminant within IFA samples further attracts to address this issue. In response, the hydrometallurgical recycling of a cobalt-bearing IFA has been studied. Thereby, approximately 98 % zinc and 96 % cobalt were leached using a 1.0 mol/L H2SO4 solution at 90 °C and 1 h of leaching time. In-depth analysis of the leaching process unveiled metals' dissolution primarily via the ion-exclusion mechanism, as evidenced by lower diffusion coefficients (between 10-9 and 10-11 m2/s) and activation energies (9.6-14.9 kJ/mol). Above 99 % separation of zinc from the cobalt-bearing leach liquor was achieved by extraction with 1.0 mol/L D2EHPA at an equilibrium pH below 3.0, followed by stripping with a 2.0 mol/L H2SO4 solution. Cobalt, remained in the raffinate was efficiently precipitated by adding a 20 % excess dosage of oxalic acid to the stoichiometric ratio of C2O42-:Co2+, resulting in only 5 mg/L cobalt left in the solution when precipitation occurred at a pH of 2.8. Additionally, the conversion of CoC2O4 to high-purity Co3O4 was conducted through heat-treatment at 600 °C. The resulting Co3O4 was mixed with Li2CO3 at a Li/Co molar ratio of 1.1, yielding a LiCoO2 precursor that exhibited good electrochemical properties with a capacity of 128 mAh/g, thus affirming the high quality of the recycled cobalt. A comprehensive life-cycle assessment of the recycling process revealed that cobalt precipitation alone contributes approximately 50 % of the total global warming potential (GWP = 4.2624 kg CO2-eq). Notably, this value is remarkably lower than the GWP reported for primary cobalt production, highlighting the environmentally-friendly approach of this recycling endeavor.

An ultrasensitive Cd2+ detection biosensor based on DNAzyme and CRISPR/Cas12a coupled with hybridization chain reaction

The detection of cadmium is essential because it poses a significant threat to human health and the environment. Recent advancements in biosensors that detect nonnucleic-acid targets using CRISPR/Cas12a in combination with aptamers or DNAzymes show promising performance. Herein, we integrated DNAzyme, hybridization chain reaction (HCR) and CRISPR/Cas12a into a single biosensor for the first time and realized the ultrasensitive detection of Cd2+. A single phosphorothioate ribonucleobase (rA)-containing oligonucleotide (PS substrate) and a Cd2+-specific DNAzyme (Cdzyme) are used for Cd2+ recognition, releasing short single-stranded DNA. Then, the HCR is triggered by the cleavage products for signal transduction and amplification. Next, the trans-cleavage activity of Cas12a is activated due to the presence of crRNA complementary strands and PAM sites in the HCR products. As a result, FQ-reporters are cleaved, and the fluorescence values can be easily read using a fluorometer, allowing Cd2+ quantification by measuring the fluorescent signal. The Cd2+ detection biosensor is ultrasensitive with a detection limit of 1.25 pM. Moreover, the biosensor shows great stability under different pH and various anion conditions. The proposed sensor was utilized for environmental water sample detection, demonstrating the dependability of the detection system. Considering the high sensitivity and reliable performance of the assay, it could be further used in environmental monitoring. In addition, the design strategy reported in this study could extend the application of CRISPR/Cas12a in heavy metal detection.

Theoretical study on the glycosidic C-C bond cleavage of 3''-oxo-puerarin

Puerarin, daidzein C-glucoside, was known to be biotransformed to daidzein by human intestinal bacteria, which is eventually converted to (S)-equol. The metabolic pathway of puerarin to daidzein by DgpABC of Dorea sp. PUE strain was reported as puerarin (1) → 3''-oxo-puerarin (2) → daidzein (3) + hexose enediolone (C). The second reaction is the cleavage of the glycosidic C-C bond, supposedly through the quinoid intermediate (4). In this work, the glycosidic C-C bond cleavage reaction of 3''-oxo-puerarin (2) was theoretically studied by means of DFT calculation to elucidate chemical reaction mechanism, along with biochemical energetics of puerarin metabolism. It was found that bioenergetics of puerarin metabolism is slightly endergonic by 4.99 kcal/mol, mainly due to the reaction step of hexose enediolone (C) to 3''-oxo-glucose (A). The result implied that there could be additional biochemical reactions for the metabolism of hexose enediolone (C) to overcome the thermodynamic energy barrier of 4.59 kcal/mol. The computational study focused on the C-C bond cleavage of 3''-oxo-puerarin (2) found that formation of the quinoid intermediate (4) was not accessible thermodynamically, rather the reaction was initiated by the deprotonation of 2''C-H proton of 3''-oxo-puerarin (2). The 2''C-dehydro-3''-oxo-puerarin (2a2C) anionic species produced hexose enediolone (C) and 8-dehydro-daidzein anion (3a8), and the latter quickly converted to daidzein through the daidzein anion (3a7). Our study also explains why the reverse reaction of C-glycoside formation from daidzein (3) and hexose enediolone (C) is not feasible.

DFT-based analysis of siderophore-metal ion interaction for efficient heavy metal remediation

Siderophores have great application potential in metal pollutant remediation because of their effective cost and friendly impact on the environment. However, the practical use of siderophores in the remediation of specific metals is rather limited because of the weak nonspecific interactions between the siderophores and different metals. Thus, screening for a siderophore with optimal interaction with a specific metal would be necessary. In this study, the interaction between metal ions and moieties that donate the oxygen ligands for the coordination of four types of siderophore (hydroxamates, catecholates, phenolates, and carboxylates) was modeled and analyzed. As revealed by DFT-based analysis, the four types of siderophore generally exhibited selection preference for different metal ions in the order Ga3+  > Al3+  > Fe3+  > Cr3+  > Ni2+  > Cu2+  > Zn2+  > Co2+  > Mn2+  > Hg2+  > Pb2+  > Cd2+, which was determined mainly by the electronegativity of the siderophore functional groups, the electronegativity of the metals, and the ionic radius of the metals, as well as the interaction between the siderophores and the metals. Moreover, the effect of linear or nonlinear (cyclic) structure on the affinity of each siderophore for different metal ions was evaluated. In most situations, metal-bound cyclic siderophores were found to be more stable than their linear counterparts. Thus, proper siderophores for the remediation of metal pollution may be rapidly screened using this model.

Cationic Divalent Metal Sites (M = Mn, Fe, Co) Operating as Both Nitrene-Transfer Agents and Lewis Acids toward Mediating the Synthesis of Three- and Five-Membered N-Heterocycles

The tripodal compounds [(TMG3trphen)MII-solv](PF6)2 (M = Mn, Fe, Co; solv = MeCN, DMF) and bipodal analogues [(TMG2biphen)MII(NCMe)x](PF6)2 (x = 3 for Mn, Fe; x = 2 for Co) and [(TMG2biphen)MIICl2] have been synthesized with ligands that feature a triaryl- or diarylmethyl-amine framework and superbasic tetramethylguanidinyl residues (TMG). The dicationic M(II) sites mediate catalytic nitrene-transfer reactions between the imidoiodinane PhI═NTs (Ts = tosyl) and a panel of styrenes in MeCN to afford aziridines and low yields of imidazolines (upon MeCN insertion) with an order of productivity that favors the bipodal over the tripodal reagents and a metal preference of Fe > Co ≥ Mn. In CH2Cl2, the more acidic Fe(II) sites favor formation of 2,4-diaryl-N-tosylpyrrolidines by means of an in situ (3 + 2) cycloaddition of the initially generated 2-aryl-N-tosylaziridine with residual styrene. In the presence of ketone, 1,3-oxazolidines can be formed in practicable yields, involving a single-pot cycloaddition reaction of alkene, nitrene, and ketone (2 + 1 + 2). Mechanistic studies indicate that the most productive bipodal Fe(II) site mediates stepwise addition of nitrene to olefins to generate aziridines with good retention of stereochemistry and further enables aziridine ring opening to unmask a 1,3-zwitterion that can undergo cycloaddition with dipolarophiles (MeCN, alkene, ketone) to afford five-membered N-heterocycles.

Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA

Structural analysis of RNA is an important and versatile tool to investigate the function of this type of molecules in the cell as well as in vitro. Several robust and reliable procedures are available, relying on chemical modification inducing RT stops or nucleotide misincorporations during reverse transcription. Others are based on cleavage reactions and RT stop signals. However, these methods address only one side of the RT stop or misincorporation position. Here, we describe Led-Seq, a new approach based on lead-induced cleavage of unpaired RNA positions, where both resulting cleavage products are investigated. The RNA fragments carrying 2', 3'-cyclic phosphate or 5'-OH ends are selectively ligated to oligonucleotide adapters by specific RNA ligases. In a deep sequencing analysis, the cleavage sites are identified as ligation positions, avoiding possible false positive signals based on premature RT stops. With a benchmark set of transcripts in Escherichia coli, we show that Led-Seq is an improved and reliable approach based on metal ion-induced phosphodiester hydrolysis to investigate RNA structures in vivo.

Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes

Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH2RR'][Cr7MF8(O2CtBu)16] with M = MnII, FeII, CoII, NiII, CuII, ZnII, CdII. Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH2RR']+. Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.

Holo-chromodulin: competition between the native Cr3+ and other biogenic cations (Fe3+, Fe2+, Mg2+, and Zn2+) for the binding sites

Chromodulin is an oligopeptide that has an essential role for the flawless functioning of insulin. Although the precise sequence of the constituent amino acid residues and the 3D structure of the molecule has not yet been deciphered, it is known that chromodulin contains only four amino acids in the ratio of Glu-: Gly: Cys: Asp- = 4: 2: 2: 2. An indispensable part for the integrity of the molecule in its active (holo-) form are four chromium cations (hence the name) in the oxidation state of 3+, positioned in two metal binding sites containing one and three Cr3+ ions. Experimental works provide some hints/clues concerning the structure of the metal centers, although their exact composition, type, and arrangement of metal ligating entities remain enigmatic. In the current study, we endeavor to unveil possible structure(s) of the Cr3+ loaded binding sites by strictly following the evidence provided by the experimental data. Well-calibrated in silico methodology for optimization and evaluation of Gibbs free energies is applied and gives strong premises for reliably deciphering the composition/structure of chromodulin metal binding sites. Additional computations reveal the advantage of choosing Cr3+ over other tri- (Fe3+) and divalent (Fe2+, Mg2+, and Zn2+) biogenic ions for securing maximum stability of the metal-occupied binding sites.

Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes

Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.

Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes

Nucleolytic ribozymes utilize general acid-base catalysis to perform phosphodiester cleavage. In most ribozyme classes, a conserved active site guanosine is positioned to act as general base, thereby activating the 2'-OH group to attack the scissile phosphate (γ-catalysis). Here, we present an atomic mutagenesis study for the pistol ribozyme class. Strikingly, "general base knockout" by replacement of the guanine N1 atom by carbon results in only 2.7-fold decreased rate. Therefore, the common view that γ-catalysis critically depends on the N1 moiety becomes challenged. For pistol ribozymes we found that γ-catalysis is subordinate in overall catalysis, made up by two other catalytic factors (α and δ). Our approach allows scaling of the different catalytic contributions (α, β, γ, δ) with unprecedented precision and paves the way for a thorough mechanistic understanding of nucleolytic ribozymes with active site guanines.

Metal-Catalyzed Hydrolysis of RNA in Aqueous Environments

The stability of RNA in aqueous systems is critical for multiple environmental applications including evaluating the environmental fate of RNA interference pesticides and interpreting viral genetic marker abundance for wastewater-based epidemiology. In addition to biological processes, abiotic reactions may also contribute to RNA loss. In particular, some metals are known to dramatically accelerate rates of RNA hydrolysis under certain conditions (i.e., 37 °C or higher temperatures, 0.15-100 mM metal concentrations). In this study, we investigated the extent to which metals catalyze RNA hydrolysis under environmentally relevant conditions. At ambient temperature, neutral pH, and ∼10 μM metal concentrations, we determined that metals that are stronger Lewis acids (i.e., lead, copper) catalyzed single-stranded (ss)RNA, whereas metals that are weaker Lewis acids (i.e., zinc, nickel) did not. In contrast, double-stranded (ds)RNA resisted hydrolysis by all metals. While lead and copper catalyzed ssRNA hydrolysis at ambient temperature and neutral pH values, other factors such as lowering the solution pH and including inorganic and organic ligands reduced the rates of these reactions. Considering these factors along with sub-micromolar metal concentrations typical of environmental systems, we determined that both ssRNA and dsRNA are unlikely to undergo significant metal-catalyzed hydrolysis in most environmental aqueous systems.

Heterodinuclear Mg(II)M(II) (M=Cr, Mn, Fe, Co, Ni, Cu and Zn) Complexes for the Ring Opening Copolymerization of Carbon Dioxide/Epoxide and Anhydride/Epoxide

The catalysed ring opening copolymerizations (ROCOP) of carbon dioxide/epoxide or anhydride/epoxide are controlled polymerizations that access useful polycarbonates and polyesters. Here, a systematic investigation of a series of heterodinuclear Mg(II)M(II) complexes reveals which metal combinations are most effective. The complexes combine different first row transition metals (M(II)) from Cr(II) to Zn(II), with Mg(II); all complexes are coordinated by the same macrocyclic ancillary ligand and by two acetate co-ligands. The complex syntheses and characterization data, as well as the polymerization data, for both carbon dioxide/cyclohexene oxide (CHO) and endo-norbornene anhydride (NA)/cyclohexene oxide, are reported. The fastest catalyst for both polymerizations is Mg(II)Co(II) which shows propagation rate constants (k_p ) of 34.7 mM^-1  s^-1 (CO₂ ) and 75.3 mM^-1  s^-1 (NA) (100 °C). The Mg(II)Fe(II) catalyst also shows excellent performances with equivalent rates for CO₂ /CHO ROCOP (k_p =34.7 mM^-1  s^-1 ) and may be preferable in terms of metallic abundance, low cost and low toxicity. Polymerization kinetics analyses reveal that the two lead catalysts show overall second order rate laws, with zeroth order dependencies in CO₂ or anhydride concentrations and first order dependencies in both catalyst and epoxide concentrations. Compared to the homodinuclear Mg(II)Mg(II) complex, nearly all the transition metal heterodinuclear complexes show synergic rate enhancements whilst maintaining high selectivity and polymerization control. These findings are relevant to the future design and optimization of copolymerization catalysts and should stimulate broader investigations of synergic heterodinuclear main group/transition metal catalysts.

Hydrated Metal Ions as Weak Bronsted Acids Show the Promoting Effects in Proton Conduction

It is well-known that the hydrated metal ions can act as Bronsted acids, which tend to donate protons increasing the acidic proton concentration in materials, as well as the proton...

Development of a DNAzyme-based colorimetric biosensor assay for dual detection of Cd2+ and Hg2

A colorimetric biosensor assay has been developed for Cd²⁺ and Hg²⁺ detection based on Cd²⁺-dependent DNAzyme cleavage and Hg²⁺-binding-induced conformational switching of the G-quadruplex fragment. Two types of multifunctional magnetic beads (Cd-MBs and Hg-MBs) were synthesized by immobilizing two functionalized DNA sequences on magnetic beads via avidin-biotin chemistry. For Cd²⁺ detection, Cd-MBs are used as recognition probes, which are modified with a single phosphorothioate ribonucleobase (rA) substrate (PS substrate) and a Cd²⁺-specific DNAzyme (Cdzyme). In the presence of Cd²⁺, the PS substrate is cleaved by Cdzyme, and single-stranded DNA is released as the signal transduction sequence. After molecular assembly with the other two oligonucleotides, duplex DNA is produced, and it can be recognized and cleaved by FokI endonuclease. Thus, a signal output component consisting of a G-quadruplex fragment is released, which catalyzes the oxidation of ABTS with the addition of hemin and H₂O₂, inducing a remarkably amplified colorimetric signal. To rule out false-positive results and reduce interference signals, Hg-MBs modified with poly-T fragments were used as Hg²⁺ accumulation probes during the course of Cd²⁺ detection. On the other hand, Hg-MBs can perform their second function in Hg²⁺ detection by changing the catalytic activity of the G-quadruplex/hemin DNAzyme. In the presence of Hg²⁺, the G-quadruplex structure in Hg-MBs is disrupted upon Hg²⁺ binding. In the absence of Hg²⁺, an intensified color change can be observed by the naked eye for the formation of intact G-quadruplex/hemin DNAzymes. The biosensor assay exhibits excellent selectivity and high sensitivity. The detection limits for Cd²⁺ and Hg²⁺ are 1.9 nM and 19.5 nM, respectively. Moreover, the constructed sensors were used to detect environmental water samples, and the results indicate that the detection system is reliable and could be further used in environmental monitoring. The design strategy reported in this study could broadly extend the application of metal ion-specific DNAzyme-based biosensors.

Metallo-inhibition of Mnx, a bacterial manganese multicopper oxidase complex

The manganese oxidase complex, Mnx, from Bacillus sp. PL-12 contains a multicopper oxidase (MCO) and oxidizes dissolved Mn(II) to form insoluble manganese oxide (MnO₂) mineral. Previous kinetic and spectroscopic analyses have shown that the enzyme's mechanism proceeds through an activation step that facilitates formation of a series of binuclear Mn complexes in the oxidation states II, III, and IV on the path to MnO₂ formation. We now demonstrate that the enzyme is inhibited by first-row transition metals in the order of the Irving-Williams series. Zn(II) strongly (K_i ~ 1.5 μM) inhibits both activation and turnover steps, as well as the rate of Mn(II) binding. The combined Zn(II) and Mn(II) concentration dependence establishes that the inhibition is non-competitive. This result is supported by electron paramagnetic resonance (EPR) spectroscopy, which reveals unaltered Mnx-bound Mn(II) EPR signals, both mono- and binuclear, in the presence of Zn(II). We infer that inhibitory metals bind at a site separate from the substrate sites and block the conformation change required to activate the enzyme, a case of allosteric inhibition. The likely biological role of this inhibitory site is discussed in the context of Bacillus spore physiology. While Cu(II) inhibits Mnx strongly, in accord with the Irving-Williams series, it increases Mnx activation at low concentrations, suggesting that weakly bound Cu, in addition to the four canonical MCO-Cu, may support enzyme activity, perhaps as an electron transfer agent.

In search of the RNA world on Mars

Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth's prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation > 4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study, we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe²⁺ , Mg²⁺ , and Mn²⁺ ) spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis (cleavage) and evaluate whether early Mars could have been permissive toward the accumulation of long-lived RNA polymers. Our results indicate that a Mg²⁺ -rich basalt sourcing metals to a slightly acidic (pH 5.4) environment mediates the slowest rates of RNA cleavage, though geologic evidence and basalt weathering models suggest aquifers on Mars would be near neutral (pH ~ 7). Moreover, the early onset of oxidizing conditions on Mars has major consequences regarding the availability of oxygen-sensitive metals (i.e., Fe²⁺ and Mn²⁺ ) due to increased RNA degradation rates and precipitation. Overall, (a) low pH decreases RNA cleavage at high metal concentrations; (b) acidic to neutral pH environments with Fe²⁺ or Mn²⁺ cleave more RNA than Mg²⁺ ; and (c) alkaline environments with Mg²⁺ dramatically cleaves more RNA while precipitates were observed for Fe²⁺ and Mn²⁺ .

Analysis of Solid-State Reaction Mechanisms with Two-Dimensional Fourier Transform Infrared Correlation Spectroscopy

The utility of two-dimensional generalized correlation spectroscopy (2D-COS) for tracking complex solid-state reactions is demonstrated using infrared spectra acquired during a photochemically induced decomposition reaction. Eleven different thin films, consisting of six monometallic and five bimetallic 2-ethylhexanoate complexes, were tracked as a function of photolysis time. Overlapping peaks in the infrared fingerprint region are readily discriminated using 2D-COS, enabling individual vibrational components to be used to distinguish whether carboxylate ligands are free/ionic or bound in a chelating, bridging, or monodentate fashion. This classification enables the decomposition mechanism to be tracked for all 11 samples, revealing that ligands bound in monodentate and bridging fashions are first converted to chelates before being lost as volatile products for all samples. The magnitude of the measured first-order rate constants for loss of chelated ligands is found to correlate linearly to the asymmetric stretching frequency of monodentate ligands but exhibits a V shape when plotted against the electronegativity of the metal center. We propose that loss of chelated ligands proceeds via C-O scission for highly electronegative transition metals but M-O scission for transition metals with low electronegativity. These results establish 2D-COS as a powerful tool to deconvolute and correlate individual components, enabling mechanistic analysis of complex chemical reactions.

Investigating the roles of the conserved Cu2+-binding residues on Brucella FtrA in producing conformational stability and functionality

Brucella is a zoonotic pathogen requiring iron for its survival and acquires this metal through the expression of several high-affinity uptake systems. Of these, the newly discovered ferrous iron transporter, FtrABCD, is proposed to take part in ferrous iron uptake. Sequence homology shows that, FtrA, the proposed periplasmic ferrous-binding component, is a P19-type protein (a periplasmic protein from C. jejuni which shows Cu2+ dependent iron affinity). Previous structural and biochemical studies on other P19 systems have established a Cu2+ dependent Mn2+ affinity as well as formation of homodimers for these systems. The Cu2+ coordinating amino acids from these proteins are conserved in Brucella FtrA, hinting towards similar properties. However, there has been no experimental evidence, till date, establishing metal affinities and the possibility of dimer formation by Brucella FtrA. Using wild-type FtrA and Cu2+-binding mutants (H65A, E67A, H118A, and H151A) we investigated the metal affinities, folding stabilities, dimer forming abilities, and the molecular basis of the Cu2+ dependence for this P19-type protein employing homology modeling, analytical gel filtration, calorimetric, and spectroscopic methods. The data reported here confirm a Cu2+-dependent, low-μM Mn2+ (Fe2+ mimic) affinity for the wild-type FtrA. In addition, our data clearly show the loss of Mn2+ affinity, and the formation of less stable protein conformations as a result of mutating these conserved Cu2+-binding residues, indicating the important roles these residues play in producing a native and functional fold of Brucella FtrA.

Mechanistic Study of Enhanced Protonation by Chromium(III) in Electrospray Ionization: A Superacid Bound to a Peptide

Addition of trivalent chromium, Cr(III), to solutions undergoing electrospray ionization (ESI) enhances protonation and leads to formation of [M + 2H]²⁺ for peptides that normally produce [M + H]⁺. This effect is explored using electronic structure calculations at the density functional theory (DFT) level to predict the energetics of various species that are potentially important to the mechanism. Gas- and solution-phase reaction free energies for glycine and its anion reacting with [Cr(III)(H₂O)₆]³⁺ and for dehydration of these species have been predicted, where glycine is used as a simple model for a peptide. For comparison, calculations were also performed with Fe(III), Al(III), Sc(III), Y(III), and La(III). Removal of water from these complexes, as would occur during the ESI desolvation process, results in species that are highly acidic. The calculated pK_a of Cr(III) with a single solvation shell is -10.8, making [Cr(III)(H₂O)₆]³⁺ a superacid that is more acidic than sulfuric acid (pK_a = -8.8). Binding to glycine requires removal of two aqua ligands, which gives [Cr(III)(H₂O)₄]³⁺ that has an extremely acidic pK_a of -28.8. Removal of additional water further enhances acidity, reaching a pK_a of -84.7 for [Cr(III)(H₂O)]³⁺. A mechanism for enhanced protonation is proposed that incorporates computational and experiment results, as well as information on the known chemistry of Cr(III), which is substitutionally inert. The initial step involves binding of [Cr(III)(H₂O)₄]³⁺ to the deprotonated C-terminus of a peptide. As the drying process during ESI strips water from the complex, the resulting superacid transfers protons to the bound peptide, eventually leading to formation of [M + 2H]²⁺.

Catalysis of Template-Directed Nonenzymatic RNA Copying by Iron(II)

The study of nonenzymatic template-directed RNA copying is the experimental basis for the search for chemistry and reaction conditions consistent with prebiotic RNA replication. The most effective model systems for RNA copying have to date required a high concentration of Mg²⁺. Recently, Fe²⁺, which was abundant on the prebiotic anoxic Earth, was shown to promote the folding of RNA in a manner similar to the case of Mg²⁺, as a result of the two cations having similar interactions with phosphate groups. These observations raise the question of whether Fe²⁺ could have promoted RNA copying on the prebiotic Earth. Here, we demonstrate that Fe²⁺ is a better catalyst and promotes faster nonenzymatic RNA primer extension and ligation than Mg²⁺ when using 2-methylimidazole activated nucleotides in slightly acidic to neutral pH solutions. Thus, it appears likely that Fe²⁺ could have facilitated RNA replication and evolution in concert with other metal cations on the prebiotic Earth.

Concerted Metal Cation Desorption and Proton Transfer on Deprotonated Silica Surfaces

The adsorption equilibrium constants of monovalent and divalent cations to material surfaces in aqueous media are central to many technological, natural, and geochemical processes. Cation adsorption-desorption is often proposed to occur in concert with proton transfer on hydroxyl-covered mineral surfaces, but to date this cooperative effect has been inferred indirectly. This work applies density functional theory-based molecular dynamics simulations of explicit liquid water/mineral interfaces to calculate metal ion desorption free energies. Monodentate adsorption of Na⁺, Mg²⁺, and Cu²⁺ on partially deprotonated silica surfaces are considered. Na⁺ is predicted to be unbound, while Cu²⁺ exhibits binding free energies to surface SiO^- groups that are larger than those of Mg²⁺. The predicted trends agree with competitive adsorption measurements on fumed silica surfaces. As desorption proceeds, Cu²⁺ dissociates one of the H₂O molecules in its first solvation shell, turning into Cu²⁺(OH^-)(H₂O)₃, while Mg remains Mg²⁺(H₂O)₆. The protonation state of the SiO^- group at the initial binding site does not vary monotonically with cation desorption.

Modular bimetallic complexes with a sulfonamido-based ligand

A series of bimetallic complexes prepared with the ligands N,N,N',N'-tetramethylethane-1,2-diamine (TMEDA) and N,N',N''-[2,2',2''-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzenesulfonamido) ([MST]3-) is described. Four diiron compounds of the formulation (TMEDA)FeII(X)-(μ-OH)-FeIIIMST were prepared, in which the X- ligands are the anions OTf-, Br-, SCN-, or N3-. Additionally, two heterobimetallic compounds of the formulation (TMEDA)MII(OTf)-(μ-OH)-FeIIIMST (MII = CoII or NiII) were synthesized. All these compounds have similar spectroscopic and structural properties. The diiron compounds exhibit perpendicular-mode electron paramagnetic resonance spectra consistent with S = 1/2 spin ground states, which is expected for high-spin FeII and FeIII centres that are antiferromagnetically coupled. The heterobimetallic (TMEDA)NiII(OTf)-(μ-OH)-FeIIIMST complex had a spin state of S = 3/2 that also resulted from antiferromagnetic coupling between the high-spin NiII and FeIII centres. The modularity of this system is further demonstrated by the substitution of the TMEDA ligand with ethylenediamine (en); for this species two equivalents of en coordinate to the FeII centre to form [(en)2FeII-(μ-OH)-FeIIIMST]OTf. These results demonstrate that a modular bimetallic system has been developed in which the key components can be modified.

Maturation processes in glass-ionomer dental cements

Glass-ionomer cements are used for a variety of tooth-repair functions in clinical dentistry. They are formed by reaction of a basic glass powder with a solution of polymeric water-soluble acid, usually polyacrylic acid. After the initial neutralization reaction, by which the cement hardens, various maturation reactions occur. Changes induced by these maturation reactions are identified as: increase in strength; reduction in plasticity; improvement in opacity; and increase in proportion of tightly bound water. In addition, in contact with the tooth, an ion-exchange interfacial layer is gradually formed. This is mechanically strong and chemically-resistant. These changes are described in the current paper, which reviews the extent to which they occur, and reports what is know about the chemistry that underlies them. Processes involving slow diffusion of various ions and of water through the set cement bring about these changes. They include a secondary setting reaction to form a phosphate-based phase, binding of water to co-ordination sites around metal cations and to a hydration sheath around the polymer molecules, and possibly reaction of water with glass particle surfaces to form silanol groups. Evidence from a wide range of literature sources is used to be build up a detailed picture of the chemistry of the maturation processes, and gaps in our understanding are highlighted. The article concludes that, given the importance of glass-ionomers in contemporary dentistry, it is important to know the extent to which such maturation processes occur in current cement formulations, and also to determine how rapidly they take place.

The Irving-Williams series and the 2-His-1-carboxylate facial triad: a thermodynamic study of Mn2+, Fe2+, and Co2+ binding to taurine/α-ketoglutarate dioxygenase (TauD)

Taurine/α-ketoglutarate (αKG) dioxygenase (TauD) is an E. coli nonheme Fe²⁺- and αKG-dependent metalloenzyme that catalyzes the hydroxylation of taurine, leading to the production of sulfite. The metal-dependent active site in TauD is formed by two histidine and one aspartate that coordinating to one face of an octahedral coordination geometry, known as the 2-His-1-carboxylate facial triad. This motif is found in many nonheme Fe²⁺ proteins, but there is limited information on the thermodynamic parameters that govern metal-ion binding to this site. Here, we report data from calorimetry and related biophysical techniques to generate complete thermodynamic profiles of Mn²⁺ and Co²⁺ binding to TauD, and these values are compared to the Fe²⁺ data reported earlier Henderson et al. (Inorg Chem 54: 2278-2283, 2015). The buffer-independent binding constants (K) were measured to be 1.6 × 10⁶, 2.4 × 10⁷, and 1.7 × 10⁹, for Mn²⁺, Fe²⁺, and Co²⁺, respectively. The corresponding ΔG° values were calculated to be - 8.4, - 10.1, and - 12.5 kcal/mol, respectively. The metal-binding enthalpy changes (ΔH) for these binding events are - 11.1 (± 0.1), - 12.2 (± 0.1), and - 16.0 (± 0.6) kcal/mol, respectively. These data are fully consistent with the Irving-Williams series, which show an increasing affinity for transition metal ions across the periodic table. It appears that the periodic increase in affinity, however, is a result of a complicated summation of enthalpy terms (including favorable metal-ion coordination processes and unfavorable ionization events) and related entropy terms.

An efficient protocol for computing the pKa of Zn-bound water

We present an efficient and accurate method for computing absolute pK_w values in Zn²⁺ complexes.

A versatile quinoxaline derivative serves as a colorimetric sensor for strongly acidic pH

A strongly acidic colorimetric pH sensor induced by the acidity of [Fe(H₂O)₆]³⁺, and single crystal to single crystal transformation between the protonated and deprotonated form.

Models for Unsymmetrical Active Sites in Metalloproteins: Structural, Redox, and Magnetic Properties of Bimetallic Complexes with MII-(μ-OH)-FeIII Cores

Bimetallic complexes are important sites in metalloproteins but are often difficult to prepare synthetically. We have previously introduced an approach to form discrete bimetallic complexes with MII-(μ-OH)-FeIII (MII = Mn, Fe) cores using the tripodal ligand N,N',N″-[2,2',2″-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzenesulfonamido) ([MST]3-). This series is extended to include the rest of the late 3d transition metal ions (MII = Co, Ni, Cu, Zn). All of the bimetallic complexes have similar spectroscopic and structural properties that reflect little change despite varying the MII centers. Magnetic studies performed on the complexes in solution using electron paramagnetic resonance spectroscopy showed that the observed spin states varied incrementally from S = 0 through S = 5/2; these results are consistent with antiferromagnetic coupling between the high-spin MII and FeIII centers. However, the difference in the MII ion occupancy yielded only slight changes in the magnetic exchange coupling strength, and all complexes had J values ranging from +26(4) to +35(3) cm-1.

Oxidative damage of 18S and 5S ribosomal RNA in digestive gland of mussels exposed to trace metals

Numerous studies have shown the ability of trace metals to accumulate in marine organisms and cause oxidative stress that leads to perturbations in many important intracellular processes, including protein synthesis. This study is mainly focused on the exploration of structural changes, like base modifications, scissions, and conformational changes, caused in 18S and 5S ribosomal RNA (rRNA) isolated from the mussel Mytilus galloprovincialis exposed to 40μg/L Cu, 30μg/L Hg, or 100μg/L Cd, for 5 or 15days. 18S rRNA and 5S rRNA are components of the small and large ribosomal subunit, respectively, found in complex with ribosomal proteins, translation factors and other auxiliary components (metal ions, toxins etc). 18S rRNA plays crucial roles in all stages of protein synthesis, while 5S rRNA serves as a master signal transducer between several functional regions of 28S rRNA. Therefore, structural changes in these ribosomal constituents could affect the basic functions of ribosomes and hence the normal metabolism of cells. Especially, 18S rRNA along with ribosomal proteins forms the decoding centre that ensures the correct codon-anticodon pairing. As exemplified by ELISA, primer extension analysis and DMS footprinting analysis, each metal caused oxidative damage to rRNA, depending on the nature of metal ion and the duration of exposure. Interestingly, exposure of mussels to Cu or Hg caused structural alterations in 5S rRNA, localized in paired regions and within loops A, B, C, and E, leading to a continuous progressive loss of the 5S RNA structural integrity. In contrast, structural impairments of 5S rRNA in mussels exposed to Cd were accumulating for the initial 5days, and then progressively decreased to almost the normal level by day 15, probably due to the parallel elevation of metallothionein content that depletes the pools of free Cd. Regions of interest in 18S rRNA, such as the decoding centre, sites implicated in the binding of tRNAs (A- and P-sites) or translation factors, and areas related to translation fidelity, were found to undergo significant metal-induced conformational alterations, leading either to loosening of their structure or to more compact folding. These modifications were associated with parallel alterations in the translation process at multiple levels, a fact suggesting that structural perturbations in ribosomes, caused by metals, pose significant hurdles in translational efficiency and fidelity.

Biochemical characterization of a new nicotinamidase from an unclassified bacterium thriving in a geothermal water stream microbial mat community

Nicotinamidases are amidohydrolases that convert nicotinamide into nicotinic acid, contributing to NAD+ homeostasis in most organisms. In order to increase the number of nicotinamidases described to date, this manuscript characterizes a nicotinamidase obtained from a metagenomic library fosmid clone (JFF054_F02) obtained from a geothermal water stream microbial mat community in a Japanese epithermal mine. The enzyme showed an optimum temperature of 90°C, making it the first hyperthermophilic bacterial nicotinamidase to be characterized, since the phylogenetic analysis of this fosmid clone placed it in a clade of uncultured geothermal bacteria. The enzyme, named as UbNic, not only showed an alkaline optimum pH, but also a biphasic pH dependence of its kcat, with a maximum at pH 9.5-10.0. The two pKa values obtained were 4.2 and 8.6 for pKes1 and pKes2, respectively. These results suggest a possible flexible catalytic mechanism for nicotinamidases, which reconciles the two previously proposed mechanisms. In addition, the enzyme showed a high catalytic efficiency, not only toward nicotinamide, but also toward other nicotinamide analogs. Its mutational analysis showed that a tryptophan (W83) is needed in one of the faces of the active site to maintain low Km values toward all the substrates tested. Furthermore, UbNic proved to contain a Fe2+ ion in its metal binding site, and was revealed to belong to a new nicotinamidase subgroup. All these characteristics, together with its high pH- and thermal stability, distinguish UbNic from previously described nicotinamidases, and suggest that a wide diversity of enzymes remains to be discovered in extreme environments.

Nature-Inspired Synthesis of Nanostructured Electrocatalysts through Mineralization of Calcium Carbonate

Biomineralization is a biogenic process that produces elaborate inorganic and organic hybrid materials in nature. Inspired by the natural process, this study explored a new mineralization approach to create nanostructured CaCO₃ films composed of amorphous CaCO₃ hemispheres by using catechol-rich polydopamine (PDA) as a biomimetic mediator. The thus synthesized biomimetic CaCO₃ was successfully transformed to nanostructured films of metal-oxide minerals, such as FeOOH, CoCO₃ , NiCO₃ , and MnOOH, through a simple procedure. The CaCO₃ -templated metal-oxide minerals functioned as efficient electrocatalysts; a CaCO₃ -templated cobalt phosphate (nanoCoPi) film exhibited high stability as a water-oxidation electrocatalyst with a current density of 1.5 mA cm^-2 . The nanostructure of nanoCoPi, consisting of individual nanoparticles (≈70 nm) and numerous internal pores (BET surface area: 3.17 m²  g^-1 ), facilitated an additional charge-transfer pathway from the electrode to individual active sites of the catalyst. This work demonstrates a plausible strategy for facile and green synthesis of nanostructured electrocatalysts through biomimetic CaCO₃ mineralization.

N-BODIPYs Come into Play: Smart Dyes for Photonic Materials

N-BODIPYs (diaminoboron dipyrromethenes) are unveiled as a new family of BODIPY dyes with huge technological potential. Synthetic access to these systems has been gained through a judicious design focused on stabilizing the involved diaminoboron chelate. Once stabilized, the obtained N-BODIPYs retain the effective photophysical behavior exhibited by other boron-substituted BODIPYs, such as O-BODIPYs. However, key bonding features of nitrogen compared to those of oxygen (enhanced bond valence and different bond directionality) open up new possibilities for functionalizing BODIPYs, allowing an increase in the number of pendant moieties (from two in O-BODIPYs, up to four in N-BODIPYs) near the chromophore and, therefore, greater control of the photophysics. As a proof of concept, the following findings are discussed: (1) the low-cost and straightforward synthesis of a selected series of N-BODIPYs; (2) their outstanding photophysical properties compared to those of related effective dyes (excellent emission signatures, including fluorescence in the solid state; notable lasing capacities in the liquid phase and when doped into polymers; improved laser performance compared to the parent F-BODIPYs); (3) the versatility of the diaminoboron moiety in allowing the generation of multifunctionalized BODIPYs, permitting access to both symmetric and asymmetric dyes; (4) the capability of such versatility to finely modulate the dye photophysics towards different photonic applications, from lasing to chemosensing.

Origins of contrasting copper coordination geometries in crystalline copper sulfate pentahydrate

Metal-aqua ion ([M(H2O)n](X+)) formation is a fundamental step in mechanisms that are central to enzymatic and industrial catalysis. Past investigations of such ions have yielded a wealth of information regarding their properties, however questions still exist involving the exact structures of these complexes. A prominent example of this is hexaaqua copper(II) ([Cu(H2O)6](2+)), with the solution versus gas-phase configurations under debate. The differences are often attributed to the intermolecular interactions between the bulk solvent and the aquated complex, resulting in structures stabilized by extended hydrogen-bonding networks. Yet solution phase systems are difficult to study due to the lack of atomic-level positional details. Crystalline solids are ideal models for comparative study, as they contain fixed structures that can be fully characterized using diffraction techniques. Here, crystalline copper sulfate pentahydrate (CuSO4·5H2O), which contains two unique copper-water geometries, was studied in order to elucidate the origin of these contrasting hydrated metal envrionments. A combination of solid-state density functional theory and low-temperature X-ray diffraction was used to probe the electronic origins of this phenomenon. This was accomplished through implementation of crystal orbital overlap population and crystal orbital Hamiltonian population analyses into a developmental version of the CRYSTAL14 software. These new computational methods help highlight the delicate interplay between electronic structure and metal-water geometries.