Developing the conversion of CO 2 in heterogeneous catalysis requires accurate characterization of the species reacting on the surface of metal oxide catalysts or supports. In this field, zirconia is used for its ability to adsorb and activate CO 2 . Nevertheless, the first and crucial step of this process, the CO 2 adsorption over ZrO 2 surfaces, is not fully understood experimentally. In particular, the diversity of surface carbonate species makes the IR analysis very complicated. This work presents a computational study on the adsorption of CO 2 on all the sites of the four most stable monoclinic ZrO 2 surfaces, (001), (011), (111), and (−111). With this exhaustive sampling of real particle surfaces, our main purpose is to characterize the surface carbonates in terms of structures, adsorption energies and nature of surface ions, coupled with a vibrational study and a Bader atomic charge analysis. Our results show that the polycoordinated carbonates are key species in the CO 2 adsorption over monoclinic ZrO 2 . The CO 2 adsorption energies largely depend on the coordination numbers of the involved Zr 4+ cations. This study offers a revisited IR assignment of the carbonate adsorbed on zirconia, showing the specificity of metal oxides with highly charged metal cations.

The development of infrared difference spectroscopy provides unprecedented insights on structures of complex molecules like metalloproteins. However, the relevant information can be hard to find among the many bands of the vibrational spectra. The ab initio modeling is very helpful to assign the frequencies to vibrational modes but it is a challenge to process the huge quantity of data into descriptors useful for experimentalists. To this end, we developed a new tool called VIBMOL allowing to analyze vibrational modes of molecules from hessian matrices calculated with common quantum chemistry codes. VIBMOL program runs on Unix machines. Through a new graphical interface, the users can calculate the normal modes of molecules, visualize them, simulate infrared spectra, and explore the Potential Energy Distribution of normal modes among any set of vibration coordinates. It is combined with an interface program (gosdmu) formatting relevant data from the GAUSSIAN program. VIBMOL code is available upon request to the authors. A discussion is provided to help the readers to choose between a large choice of different software and it shows how VIBMOL can make the IR assignment easier in the context of collaborations with experimentalists.

Oxalate ligands are found in many classes of materials, including energy-storage materials and biominerals like hydrated calcium-oxalates. 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 mechanochemical saponification. Then, the use of 17O-enriched oxalates for the synthesis of the biologically relevant calcium-oxalate monohydrate (COM) phase is presented, enabling the analysis of its structure and heat-induced phase transitions by high-resolution 17O solid-state NMR. NMR studies of the low-temperature COM form (LT-COM), using magnetic fields varying 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 oxalate ligands to be resolved, with a tentative assignment proposed. Then, the structural changes occurring upon heat treatment of COM were followed by high-resolution 17O solid-state NMR, providing new insight into the structures of the high-temperature form (HT-COM) and anhydrous calcium oxalate alpha-phase (alpha-COA), including the presence of structural disorder in the latter case. Overall, this work highlights the ease associated with 17O-isotopic enrichment of oxalate oxygens, and how it enables the study of oxalate structures (including materials of biological relevance) at high-resolution via solid-state NMR, in the frame of “NMR-crystallography” investigations.

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

Calcium oxalate minerals of 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, 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 studying the crystallographic structure of biologically relevant minerals like calcium oxalates.

Among the techniques to reveal the chemistry, structure, and dynamics of surfaces, tip-enhanced Raman spectroscopy (TERS) occupies a unique position for the investigation of nonmetallic nanomaterials: it provides a wealth of information of Raman spectroscopy even under ambient conditions with the opportunity for spatial resolution below the diffraction limit. The high sensitivity of the optical near field to surfaces has been exploited on self-assembled monolayers on multiple occasions, and yet, the potential for the investigation of crystalline surfaces remains to be unfolded. Using strontium titanate (SrTiO3) as a model system, we demonstrate that TERS does not only provide insight into surface symmetries but also activates otherwise symmetry-forbidden modes. The bulk phase of strontium titanate is Raman-inactive, and the optical far field therefore does not provide any first-order Raman signature: as a consequence, any peak in TERS configuration originates from the optical near field, confined to a few nanometers at the apex of the tip. We observe first-order Raman peaks interpreted as TO2, TO4, and LO4 phonon modes and the strong field enhancement of both infrared-active LO3 and Raman surface modes in agreement with density functional theory (DFT) calculations. The intensity enhancement of the surface modes shows the sensitivity of TERS to monitor surface relaxation effects associated with structural phase transformations into, e.g., a polar phase, and to detect surface reconstructions that are known to be crucial for photocatalytic activity.

Two mechanochemical procedures for 17O/18O-isotope labeling of fatty acids are reported: a carboxylic acid activation/hydrolysis approach and a saponification approach.

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.

Resistance to β-lactam antibiotics in Gram-negatives producing metallo-β-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 β-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.

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‐β‐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 Δ E values and their contributions in the zinc cores, with and without TZT, totaling 30 complexes. With one exception, the Δ E (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. Δ E (SIBFA) could closely reproduce Δ E (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 Δ E (SIBFA) and correlated multipoles and polarizabilities. Closely reproducing Δ E (QC) and the contrasting trends of its individual contributions should enable for dependable free energy perturbation studies and comparisons to recent experimental Δ G values, limiting as much as possible the reliance on error compensations.

Zeolite materials have complex structures that can be determined by X-ray diffraction (XRD), but characterizing the nonperiodic defects, the distribution of the aluminum atoms, and the position of the exchanged cations remain a challenge. It was shown that quantum chemistry methods (QMs) are well suited to predict the structure, even with low symmetry. Here, QMs were used to determine the location and coordination of Na-I and Cu-I cations in Si-rich faujasites of Y-type (with moderate Si/AI ratio) and Al-rich faujasites of X-type (Si/Al = 1). Focusing on the first shell of the metal site, we used QM analysis tools to study the various distortions induced by the presence of Al in the rings of faujasites. Such microscopic data were not accessible using experimental XRD methods. In contrast, using the present theoretical approach, it was possible to predict the absence of symmetry at the atomic level and that sites I were not occupied by Na-I nor by Cu-I cations, even for Al-rich faujasites of X-type. The infrared CO probe was used to analyze the interaction of both Na-I and Cu-I with the zeolite framework. Single CO adsorption on Na-I and Cu-I via the carbon atom showed that the calculated nu(CO) stretching frequency bands are mainly upshifted in comparison with isolated CO. The vco stretching frequency range was predicted to be larger for Cu-I than that for Na-I, and the bandwidth would be affected by different Al distributions in the six-membered rings (6MR): the more the Al atoms in the 6MR, the larger the bandwidth. To gain insights into the metal bonding picture with its neighbors, we performed natural bond orbital (NBO) analysis combined with the quantum theory of atoms in molecules and electron localization function topological analyses (QTAIM and ELF methods, respectively). While it is generally reported that Na cations provide electrostatic interactions with zeolite materials, Cu cations are often assumed to favor covalent interactions. The upshifting of the calculated nu(CO) stretching frequency and our topological analyses rather indicated that the interactions of Na-I and Cu-I with the oxygen atoms of the hosted zeolite were mainly ionic with a weak covalent character in the case of Cu-I. The adsorption of CO on Na-I proceeds via an ionic Na center dot center dot center dot C interaction, while for Cu-I, the Cu center dot center dot center dot CO bond was calculated to be dative with a strong polar character. Whatever the Lewis metal cation, Cu-I or Na-I, the present topological analyses predict that their interactions with the O atoms of the zeolite were ionic.

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-β-lactamases (MBLs), which represent major resistance determinants to β-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 β-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.

Periodic mesoporous organosilica nanoparticles emerge as promising vectors for nanomedicine applications. Their properties are very different from those of well‐known mesoporous silica nanoparticles as there is no silica source for their synthesis. So far, they have only been synthesized from small bis‐silylated organic precursors. However, no studies employing large stimuli‐responsive precursors have been reported on such hybrid systems yet. Here, the synthesis of porphyrin‐based organosilica nanoparticles from a large octasilylated metalated porphyrin precursor is described for applications in near‐infrared two‐photon‐triggered spatiotemporal theranostics. The nanoparticles display unique interconnected large cavities of 10–80 nm. The framework of the nanoparticles is constituted with J‐aggregates of porphyrins, which endows them with two‐photon sensitivity. The nanoparticle efficiency for intracellular tracking is first demonstrated by the in vitro near‐infrared imaging of breast cancer cells. After functionalization of the nanoparticles with aminopropyltriethoxysilane, two‐photon‐excited photodynamic therapy in zebrafish is successfully achieved. Two‐photon photochemical internalization in cancer cells of the nanoparticles loaded with siRNA is also performed for the first time. Furthermore, siRNA targeting green fluorescent protein complexed with the nanoparticles is delivered in vivo in zebrafish embryos, which demonstrates the versatility of the nanovectors for biomedical applications.

Cu-SSZ-13 efficiently catalyzes the selective catalytic reduction (SCR) of NO by NH3 but the structure of the active site and, particularly, the redox state of the copper (+I or +II) is still debated. This paper focuses on the possible contribution of Cu-I species using quantum chemistry of adsorption and co-adsorption of NH3 and H2O on Cu-I species. The calculations show that Cu-I clearly migrates upon adsorption of NH3 and H2O. All the Cu-I complexes sit in the cage containing the 8 MR and interact with the zeolite framework through several H-bonds. In the experimental temperature and pressure domain of SCR conditions, calculated phase diagrams show that a coordination number of two is predicted for the co-adsorption of NH3 and H2O on Cu-I. Finally, the calculated phase diagrams of Cu-I-SSZ-13 are discussed together with discussed together with those of Cu-II-SSZ-13 and recent experimental characterizations, providing a wider picture of the real catalyst in SCR conditions.

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-β-lactamases (MBL), an emerging class of Zn-dependent bacterial enzymes, which by cleaving the β-lactam bond of most β-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.

Despite the extensive range of investigations on boronic acids (R-B(OH)2), some aspects of their reactivity still need to be explored. This is the case for the coordination chemistry of boronate anions (R-B(OH)3−), which has only recently been started to be studied. The purpose of this review is to summarize some of the key features of boronate ligands (and of their cyclic derivatives, benzoxaborolates) in materials: (i) coordination properties; (ii) spectroscopic signatures; and (iii) emerging applications.

The determination of pK(a) 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 pK(a) values calculated with an accuracy within 0.5-1.0 pK(a) unit and then on the chalenging nicotianamine polyacid with six pK(a) values. This approach is particularly well suited for such a complex system including both zwitterionic structures and unknown experimental pK(a) values.

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.