High-Resolution 17O Solid-State NMR as a Unique Probe for Investigating Oxalate Binding Modes in Materials: The Case Study of Calcium Oxalate Biominerals.

Oxalate ligands are found in many classes of materials, including energy storage materials and biominerals. Determining their local environments at the atomic scale is thus paramount to establishing the structure and properties of numerous phases. Here, we show that high-resolution 17O solid-state NMR is a valuable asset for investigating the structure of crystalline oxalate systems. First, an efficient 17O-enrichment procedure of oxalate ligands is demonstrated using mechanochemistry. Then, 17O-enriched oxalates were used for the synthesis of the biologically relevant calcium oxalate monohydrate (COM) phase, enabling the analysis of its structure and heat-induced phase transitions by high-resolution 17O NMR. Studies of the low-temperature COM form (LT-COM), using magnetic fields from 9.4 to 35.2 T, as well as 13C-17O MQ/D-RINEPT and 17O{1H} MQ/REDOR experiments, enabled the 8 inequivalent oxygen sites of the oxalates to be resolved, and tentatively assigned. The structural changes upon heat treatment of COM were also followed by high-resolution 17O NMR, providing new insight into the structures of the high-temperature form (HT-COM) and anhydrous calcium oxalate α-phase (α-COA), including the presence of structural disorder in the latter case. Overall, this work highlights the ease associated with 17O-enrichment of oxalate oxygens, and how it enables high-resolution solid-state NMR, for "NMR crystallography" investigations.

Correction to "First Direct Insight into the Local Environment and Dynamics of Water Molecules in the Whewellite Mineral Phase: Mechanochemical Isotopic Enrichment and High-Resolution 17O and 2H NMR Analyses".

[This corrects the article DOI: 10.1021/acs.jpcc.2c02070.].

First Direct Insight into the Local Environment and Dynamics of Water Molecules in the Whewellite Mineral Phase: Mechanochemical Isotopic Enrichment and High-Resolution 17O and 2H NMR Analyses.

Calcium oxalate minerals of the general formula CaC2O4 . xH2O are widely present in nature and usually associated with pathological calcifications, constituting up to 70-80% of the mineral component of renal calculi. The monohydrate phase (CaC2O4 .H2O, COM) is the most stable form, accounting for the majority of the hydrated calcium oxalates found. These mineral phases have been studied extensively via X-ray diffraction and IR spectroscopy and, to a lesser extent, using 1H, 13C, and 43Ca solid-state NMR spectroscopy. However, several aspects of their structure and reactivity are still unclear, such as the evolution from low- to high-temperature COM structures (LT-COM and HT-COM, respectively) and the involvement of water molecules in this phase transition. Here, we report for the first time a 17O and 2H solid-state NMR investigation of the local structure and dynamics of water in the COM phase. A new procedure for the selective 17O- and 2H-isotopic enrichment of water molecules within the COM mineral is presented using mechanochemistry, which employs only microliter quantities of enriched water and leads to exchange yields up to ∼30%. 17O NMR allows both crystallographically inequivalent water molecules in the LT-COM structure to be resolved, while 2H NMR studies provide unambiguous evidence that these water molecules are undergoing different types of motions at high temperatures without exchanging with one another. Dynamics appear to be essential for water molecules in these structures, which have not been accounted for in previous structural studies on the HT-COM structure due to lack of available tools, highlighting the importance of such NMR investigations for refining the overall knowledge on biologically relevant minerals like calcium oxalates.

Cost-efficient and user-friendly 17O/18O labeling procedures of fatty acids using mechanochemistry.

Two mechanochemical procedures for 17O/18O-isotope labeling of fatty acids are reported: a carboxylic acid activation/hydrolysis approach and a saponification approach. The latter route allowed first-time enrichment of important polyunsaturated fatty acids (PUFAs) including docosahexaenoic acid (DHA). Overall, a total of 9 pure labeled products were isolated in high yields (≥80%) and with high enrichment levels (≥37% average labeling of C=O and C-OH carboxylic oxygen atoms), under mild conditions, and in short time (

Intermolecular interactions of the extended recognition site of VIM-2 metallo-ß-lactamase with 1,2,4-triazole-3-thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio QC.

Molecular dynamics on the complexes of inhibitors with Zn-metalloproteins are a privileged area of applications of polarizable molecular mechanics potentials. With which accuracy could these reproduce the QC intermolecular interaction energies in the two mono-zinc cores and in the dizinc core, toward full-fledged MD simulations on the entire protein complexes? We considered the complexes of the extended recognition site of a Zn-dependent metallo-ß-lactamase, VIM-2, produced by bacteria responsible for nosocomial infections, with five newly synthesized inhibitors sharing an original dizinc binding group, 1,2,4-triazole-3-thione (TZT). We considered the energy-minimized structures of each of the five VIM-2 complexes obtained with the SIBFA potential. Energy decomposition analyses (EDA) at the HF level enabled to compare the QC and the SIBFA ΔE values and their contributions in the zinc cores, with and without TZT, totaling 30 complexes. With one exception, the ΔE(QC) values were reproduced with relative errors <1.5%. We next considered the complex of the entire inhibitors with an extended model of VIM-2 recognition site, totaling up to 280 atoms. ΔE(SIBFA) could closely reproduce ΔE(QC). EDA analyses were resumed on the complexes of each inhibitor arm with its interacting VIM-2 residues. As a last step, EDA results at correlated levels were analyzed for the mono- and dizinc sites enabling comparisons with dispersion-augmented ΔE(SIBFA) and correlated multipoles and polarizabilities. Closely reproducing ΔE(QC) and the contrasting trends of its individual contributions should enable for dependable free energy perturbation studies and comparisons to recent experimental ΔG values, limiting as much as possible the reliance on error compensations.

Unveiling the Structure and Reactivity of Fatty-Acid Based (Nano)materials Thanks to Efficient and Scalable 17O and 18O-Isotopic Labeling Schemes.

Fatty acids are ubiquitous in biological systems and widely used in materials science, including for the formulation of drugs and the surface-functionalization of nanoparticles. However, important questions regarding the structure and reactivity of these molecules are still to be elucidated, including their mode of binding to certain metal cations or materials surfaces. In this context, we have developed novel, efficient, user-friendly, and cost-effective synthetic protocols based on ball-milling, for the 17O and 18O isotopic labeling of two key fatty acids which are widely used in (nano)materials science, namely stearic and oleic acid. Labeled molecules were analyzed by 1H and 13C solution NMR, IR spectroscopy, and mass spectrometry (ESI-TOF and LC-MS), as well as 17O solid state NMR (for the 17O labeled species). In both cases, the labeling procedures were scaled-up to produce up to gram quantities of 17O- or 18O-enriched molecules in just half-a-day, with very good synthetic yields (all ≥84%) and enrichment levels (up to an average of 46% per carboxylic oxygen). The 17O-labeled oleic acid was then used for the synthesis of a metal soap (Zn-oleate) and the surface-functionalization of ZnO nanoparticles (NPs), which were characterized for the first time by high-resolution 17O NMR (at 14.1 and 35.2 T). This allowed very detailed insight into (i) the coordination mode of the oleate ligand in Zn-oleate to be achieved (including information on Zn···O distances) and (ii) the mode of attachment of oleic-acid at the surface of ZnO (including novel information on its photoreactivity upon UV-irradiation). Overall, this work demonstrates the high interest of these fatty acid-enrichment protocols for understanding the structure and reactivity of a variety of functional (nano)materials systems using high resolution analyses like 17O NMR.

4-Amino-1,2,4-triazole-3-thione-derived Schiff bases as metallo-ß-lactamase inhibitors.

Resistance to ß-lactam antibiotics in Gram-negatives producing metallo-ß-lactamases (MBLs) represents a major medical threat and there is an extremely urgent need to develop clinically useful inhibitors. We previously reported the original binding mode of 5-substituted-4-amino/H-1,2,4-triazole-3-thione compounds in the catalytic site of an MBL. Moreover, we showed that, although moderately potent, they represented a promising basis for the development of broad-spectrum MBL inhibitors. Here, we synthesized and characterized a large number of 4-amino-1,2,4-triazole-3-thione-derived Schiff bases. Compared to the previous series, the presence of an aryl moiety at position 4 afforded an average 10-fold increase in potency. Among 90 synthetic compounds, more than half inhibited at least one of the six tested MBLs (L1, VIM-4, VIM-2, NDM-1, IMP-1, CphA) with Ki values in the µM to sub-µM range. Several were broad-spectrum inhibitors, also inhibiting the most clinically relevant VIM-2 and NDM-1. Active compounds generally contained halogenated, bicyclic aryl or phenolic moieties at position 5, and one substituent among o-benzoic, 2,4-dihydroxyphenyl, p-benzyloxyphenyl or 3-(m-benzoyl)-phenyl at position 4. The crystallographic structure of VIM-2 in complex with an inhibitor showed the expected binding between the triazole-thione moiety and the dinuclear centre and also revealed a network of interactions involving Phe61, Tyr67, Trp87 and the conserved Asn233. Microbiological analysis suggested that the potentiation activity of the compounds was limited by poor outer membrane penetration or efflux. This was supported by the ability of one compound to restore the susceptibility of an NDM-1-producing E. coli clinical strain toward several ß-lactams in the presence only of a sub-inhibitory concentration of colistin, a permeabilizing agent. Finally, some compounds were tested against the structurally similar di-zinc human glyoxalase II and found weaker inhibitors of the latter enzyme, thus showing a promising selectivity towards MBLs.

4-(N-Alkyl- and -Acyl-amino)-1,2,4-triazole-3-thione Analogs as Metallo-ß-Lactamase Inhibitors: Impact of 4-Linker on Potency and Spectrum of Inhibition.

To fight the increasingly worrying bacterial resistance to antibiotics, the discovery and development of new therapeutics is urgently needed. Here, we report on a new series of 1,2,4-triazole-3-thione compounds as inhibitors of metallo-ß-lactamases (MBLs), which represent major resistance determinants to ß-lactams, and especially carbapenems, in Gram-negative bacteria. These molecules are stable analogs of 4-amino-1,2,4-triazole-derived Schiff bases, where the hydrazone-like bond has been reduced (hydrazine series) or the 4-amino group has been acylated (hydrazide series); the synthesis and physicochemical properties thereof are described. The inhibitory potency was determined on the most clinically relevant acquired MBLs (IMP-, VIM-, and NDM-types subclass B1 MBLs). When compared with the previously reported hydrazone series, hydrazine but not hydrazide analogs showed similarly potent inhibitory activity on VIM-type enzymes, especially VIM-2 and VIM-4, with Ki values in the micromolar to submicromolar range. One of these showed broad-spectrum inhibition as it also significantly inhibited VIM-1 and NDM-1. Restoration of ß-lactam activity in microbiological assays was observed for one selected compound. Finally, the binding to the VIM-2 active site was evaluated by isothermal titration calorimetry and a modeling study explored the effect of the linker structure on the mode of binding with this MBL.

Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-ß-Lactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry.

In the context of the SIBFA polarizable molecular mechanics/dynamics (PMM/PMD) procedure, we report the calibration and a series of validation tests for the 1,2,4-triazole-3-thione (TZT) heterocycle. TZT acts as the chelating group of inhibitors of dizinc metallo-ß-lactamases (MBL), an emerging class of Zn-dependent bacterial enzymes, which by cleaving the ß-lactam bond of most ß-lactam antibiotics are responsible for the acquired resistance of bacteria to these drugs. Such a study is indispensable prior to performing PMD simulations of complexes of TZT-based inhibitors with MBL's, on account of the anchoring role of TZT in the dizinc MBL recognition site. Calibration was done by comparisons to energy decomposition analyses (EDA) of high-level ab initio QC computations of the TZT complexes with two probes: Zn(II), representative of "soft" dications, and water, representative of dipolar molecules. We performed distance variations of the approach of each probe to each of the two TZT atoms involved in Zn ligation, the S atom and the N atom ortho to it, so that each SIBFA contribution matches its QC counterpart. Validations were obtained by performing in- and out-of-plane angular variations of Zn(II) binding in monoligated Zn(II)-TZT complexes. The most demanding part of this study was then addressed. How well does ΔE(SIBFA) and its individual contributions compare to their QC counterparts in the dizinc binding site of one MBL, L1, whose structure is known from high-resolution X-ray crystallography? Six distinct complexes were considered, namely each separate monozinc site, and the dizinc site, whether ligated or unligated by TZT. Despite the large magnitude of the interaction energies, in all six complexes ΔE(SIBFA) can match ΔE(QC) with relative errors <2% and the proper balance of individual energy contributions. The computations were extended to the dizinc site of another MBL, VIM-2, and its complexes with two other TZT analogues. ΔE(SIBFA) faithfully reproduced ΔE(QC) in terms of magnitude, ranking of the three ligands, and trends of the separate energy contributions. A preliminary extension to correlated calculations is finally presented. All these validations should enable a secure design of a diversity of TZT-containing MBL inhibitors: a structurally and energetically correct anchoring of TZT should enable all other inhibitor groups to in turn optimize their interactions with the other target MBL residues.

Hydrophobic α,α-Disubstituted Disilylated TESDpg Induces Incipient 310-Helix in Short Tripeptide Sequence.

To evaluate the contribution of triethylsilyl α,α-di-n-propylglycine, namely TESDpg, to induce a defined secondary structure, we have prepared model tripeptides in which TESDpg was inserted in three different positions. Studies in solid state and in solution with adapted techniques showed that TESDpg was able to induce a nascent 310 helix in both crystal and solution states.

Coordination complexes of 4-methylimidazole with ZnII and CuII in gas phase and in water: a DFT study.

A quantum chemistry study of mononuclear metal coordination with four 4-methylimidazole ligands (4-MeIm) was investigated. The four complexes [Cu(4-MeIm)4]2+, [Cu(4-MeIm)4, H2O]2+, [Zn(4-MeIm)4]2+ and [Zn(4-MeIm)4, H2O]2+ were studied with particular attention to the Nπ or Nτ possible coordinations of the 4-MeIm ring with the metals, using different DFT methods. The results suggest that the Nτ coordination of 4-MeIm ring to ZnII or CuII is more favorable whatever the level of calculation. In contrast, the addition of one water molecule in the first coordination sphere of the metal ions provides five-coordinated complexes showing no Nπ or Nτ preferences. There is good agreement between the DFT-calculated structure and those available experimentally. When metal ions are four-fold coordinated, they adopt a tetrahedral geometry. When CuII and ZnII are five-fold coordinated, highly symmetric structures or intermediate structures are calculated. Similar energies are calculated for different structures, suggesting flat potential energy surfaces. The addition of implicit solvent modifies the calculated first coordination sphere, especially for [Cu(4-MeIm)4, H2O]2+ structures. The QTAIM and ELF topological analyses of the interaction between CuII and the neutral ligands, clearly indicate a dative bonding with a strong ionic character.

Prediction of pKa Using DFT: the Nicotianamine Polyacid Example.

The determination of pKa values for molecules containing multiple acidic groups in solution is challenging both experimentally and theoretically. We propose a general method to obtain these values by combining a graphical analysis based on a predominance diagram, for amino acids and nicotianamine polyacid, with first principle DFT calculations. Implicit and semiexplicit water solvent models were included to account for solvation. This strategy enables the investigation of the protonation states of compounds containing acidic moieties in solution depending on the pH domain. The method was first validated on a set of amino acids with pKa values calculated with an accuracy within 0.5-1.0 pKa unit and then on the chalenging nicotianamine polyacid with six pKa values. This approach is particularly well suited for such a complex system including both zwitterionic structures and unknown experimental pKa values.

Silaproline helical mimetics selectively form an all-trans PPII helix.

The polyproline II helix (PPII) is increasingly recognized as an important element in peptide and protein structures. The discovery of pertinent PPII peptidomimetics is of great interest to tune physical properties of the targeted structure. A series of silaproline oligomers from dimer to pentamer were synthesized. CD studies, NMR spectroscopy and molecular modeling revealed that the ribbon preferentially populates the polyproline type II secondary structure in both [D]chloroform and [D4 ]MeOH. The characteristics of this new lipophilic PPII-like helix were determined.

Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: bimetallic binding site and structured waters.

The existence of a network of structured waters in the vicinity of the bimetallic site of Cu/Zn-superoxide dismutase (SOD) has been inferred from high-resolution X-ray crystallography. Long-duration molecular dynamics (MD) simulations could enable to quantify the lifetimes and possible interchanges of these waters between themselves as well as with a ligand diffusing toward the bimetallic site. The presence of several charged or polar ligands makes it necessary to resort to second-generation polarizable potentials. As a first step toward such simulations, we benchmark in this article the accuracy of one such potential, sum of interactions between fragments Ab initio computed (SIBFA), by comparisons with quantum mechanics (QM) computations. We first consider the bimetallic binding site of a Cu/Zn-SOD, in which three histidines and a water molecule are bound to Cu(I) and three histidines and one aspartate are bound to Zn(II). The comparisons are made for different His6 complexes with either one or both cations, and either with or without Asp and water. The total net charges vary from zero to three. We subsequently perform preliminary short-duration MD simulations of 296 waters solvating Cu/Zn-SOD. Six representative geometries are selected and energy-minimized. Single-point SIBFA and QM computations are then performed in parallel on model binding sites extracted from these six structures, each of which totals 301 atoms including the closest 28 waters from the Cu metal site. The ranking of their relative stabilities as given by SIBFA is identical to the QM one, and the relative energy differences by both approaches are fully consistent. In addition, the lowest-energy structure, from SIBFA and QM, has a close overlap with the crystallographic one. The SIBFA calculations enable to quantify the impact of polarization and charge transfer in the ranking of the six structures. Five structural waters, which connect Arg141 and Glu131, are endowed with very high dipole moments (2.7-3.0 Debye), equal and larger than the one computed by SIBFA in ice-like arrangements (2.7 D).

Electrochemically induced far-infrared difference spectroscopy on metalloproteins using advanced synchrotron technology.

New information on a protein's structure, intra- and intermolecular hydrogen bonds, or metal-ligand bond properties can be unraveled in the far-infrared (far-IR)-terahertz-domain (600-3 cm(-1) or 18-0.1 THz). In this study, we compare the performances of thermal sources with synchrotron far-IR to record reaction-induced Fourier transform infrared (FT-IR) difference signals with proteins in solution. Using the model protein Cu-azurin placed in a short path length electrochemical cell adapted for transmission spectroscopy in vacuum-purged optics, we show that minute spectral shifts induced by metal isotope labeling or temperature changes are detected using the far-IR beamline AILES of the synchrotron SOLEIL. On one hand, these data allow us to identify modes involving Cu-ligand vibrations and pave the way for the analysis of metal sites or metal redox states of proteins not amenable to resonance Raman spectroscopy. On another hand, small band shifts or changes in band intensity upon temperature modifications show that far-IR difference spectroscopy allows one to extract from a complex background hydrogen-bonding signatures directly relevant to the protein function. For Cu-azurin, a temperature-sensitive IR mode involving Cu(II)-His vibrations points to the role of a hydrogen bond between a Cu histidine ligand and the water solvent in tuning the Cu(II)-histidine bond properties. Furthermore, these experimental data support the possible role of a His117-water interaction in electron-transfer activity of Cu-azurin proposed by theoretical studies.

Boronate ligands in materials: determining their local environment by using a combination of IR/solid-state NMR spectroscopies and DFT calculations.

Boronic acids (R-B(OH)(2)) are a family of molecules that have found a large number of applications in materials science. In contrast, boronate anions (R-B(OH)(3)(-)) have hardly been used so far for the preparation of novel materials. Here, a new crystalline phase involving a boronate ligand is described, Ca[C(4)H(9)-B(OH)(3)](2), which is then used as a basis for the establishment of the spectroscopic signatures of boronates in the solid state. The phase was characterized by IR and multinuclear solid-state NMR spectroscopy ((1)H, (13)C, (11)B and (43)Ca), and then modeled by periodic DFT calculations. Anharmonic OH vibration frequencies were calculated as well as NMR parameters (by using the Gauge Including Projector Augmented Wave--GIPAW--method). These data allow relationships between the geometry around the OH groups in boronates and the IR and (1)H NMR spectroscopic data to be established, which will be key to the future interpretation of the spectra of more complex organic-inorganic materials containing boronate building blocks.

Profiling the active site of a copper enzyme through its far-infrared fingerprint.

Vibrations of the metal active site of the Cu,Zn-superoxide dismutase enzyme were analyzed by far-infrared difference spectroscopy and theoretical normal mode calculation. Both electrochemically triggered Cu(I) and Cu(II) redox states show well-defined infrared vibrational modes, notably modes of the histidine ligands, the Cu(II)-His(61)-Zn(II) bridge and of the water pseudo-ligand.

Theoretical evidence of the observed kinetic order dependence on temperature during the N(2)O decomposition over Fe-ZSM-5.

The characterization of Fe/ZSM5 zeolite materials, the nature of Fe-sites active in N(2)O direct decomposition, as well as the rate limiting step are still a matter of debate. The mechanism of N(2)O decomposition on the binuclear oxo-hydroxo bridged extraframework iron core site [Fe(II)(mu-O)(mu-OH)Fe(II)](+) inside the ZSM-5 zeolite has been studied by combining theoretical and experimental approaches. The overall calculated path of N(2)O decomposition involves the oxidation of binuclear Fe(II) core sites by N(2)O (atomic alpha-oxygen formation) and the recombination of two surface alpha-oxygen atoms leading to the formation of molecular oxygen. Rate parameters computed using standard statistical mechanics and transition state theory reveal that elementary catalytic steps involved into N(2)O decomposition are strongly dependent on the temperature. This theoretical result was compared to the experimentally observed steady state kinetics of the N(2)O decomposition and temperature-programmed desorption (TPD) experiments. A switch of the reaction order with respect to N(2)O pressure from zero to one occurs at around 800 K suggesting a change of the rate determining step from the alpha-oxygen recombination to alpha-oxygen formation. The TPD results on the molecular oxygen desorption confirmed the mechanism proposed.

Vibrational modeling of copper-histamine complexes: metal-ligand IR modes investigation.

Recent reports on proteins and related models show that vibrational spectroscopy in the far-infrared domain is a promising technique to characterize metal sphere coordination in proteins. The low-frequency modes are however complex, and there is a need to develop the analysis of metal sites by means of quantum chemical calculations as a support for useful interpretation of the far-IR data. In this study, we determined vibrational properties for systems containing Cu(II)-N(Imidazole) interactions present in many biological complexes by means of quantum chemical calculations and confronted the normal mode description with available experimental data. Analysis of the [Cu(histamine)]2+ complex led us to conclude that the anharmonic contributions are negligible in the far-IR domain. Geometry optimizations and vibrational frequency calculations of [Cu(hm)]2+ and [Cu(hm)2(ClO4)2] complexes were compared using various hybrid DFT functionals and basis sets. These investigations stressed the need of potential energy distribution calculations (PED) to assign the vibrational modes, to obtain an overall description of the vibration modes, and to efficiently compare the methods. Comparison of calculation methods with the B3LYP/6-31+G(d,p) and B3LYP/6-311+G(2d,2p) methods and with available experimental data showed that the B3LYP/6-31G(d,p) level of theory provides accurate predictions of the normal mode frequencies and assignments. These comparisons also enlighten that theoretical investigations of 2H- and 65Cu-labeled [Cu(hm)2(ClO4)2] complexes give with a very good accuracy the band shifts of the labeled copper-histamine derivatives. The theoretical calculations combined with experimental data allowed us to predict and calculate with good accuracy the values and assignments of the low-frequency IR modes, notably those involving metal contribution.