Orthogonal effect of exchange and correlation parameters in density functional theory to compute geometric and spectroscopic quantities.

The influence of the composition of the functional used for density functional theory computations on one structural parameter (a dihedral angle) and a spectroscopic parameter (absorption wavelength) is assessed in this study on the basis of two molecules (flavonols). In this kind of molecules, these two parameters should be correlated according to the nature of the electronic transition involved. However, it is shown herein that by varying the proportion of true exchange and correlation while building a functional, it is possible to obtain independently a large range of values for these parameters without any relation with the underlying real values. Therefore, it is concluded that the choice of a functional after a benchmark, especially using user-defined functionals, should be carried out with great care to avoid such effects.

A Picosecond Time-Resolved Spectroscopic Investigation of the Effect of pH on Morin Fluorescence.

In this work, we investigated for the first time morin in MeOH at different pH values by picosecond time-resolved fluorescence. We identified the two species responsible for the fluorescence at low and high pH. The solvated morin-solvent hydrogen-bonded complex has been experimentally observed for the first time. We give also the typical fluorescence spectra as well as the fluorescence lifetimes of the probable emitting species. In this work we put forward new insights concerning the contribution of free morin to the fluorescence. We hope that these new data improve the accuracy of the interpretation of the cation:morin complexes titration using fluorescence signal.

pH dependency of the structural and photophysical properties of the atypical 2',3-dihydroxyflavone.

2',3-Dihydroxyflavone (2'3HF) is a natural flavonol that has barely ever been studied, however the scarce studies of its physico-chemical properties have highlighted its atypical behaviour. We present a structural and spectral study of 2'3HF, performed using UV-visible absorption and fluorescence spectroscopies, coupled with DFT and TD-DFT calculations. Although its structure is close to that of 3-hydroxyflavone, 2'3HF shows a much lower pK a value. We show that the origin of this particularity is the substitution by a hydroxyl group on position 2', that induces a stronger inter-ring interaction weakening the bonding of the proton at position 3. The main absorption band of the is red-shifted upon deprotonation. The remaining proton is highly bonded in between oxygen atoms 3 and 2', making the second deprotonation unattainable in methanol. The neutral form can undergo an excited-state intramolecular proton transfer to emit dual fluorescence by the normal and tautomer forms. We suggested five geometries to be the sources of the emission bands, and showed that the energy barriers to interconversions were almost null. The anion is also fluorescent. The Stokes shifts for the neutral normal and anion species are extremely high, that can be explained by the conformational rearrangement, as the species go from twisted in the ground-state, to planar in the excited-state. Finally, another emission band is evidenced when exciting in the vicinity of the absorption maximum of the anion species in acidic medium. We suggest an aggregate with the solvent to be the origin of the emission.

Spectroscopic and theoretical study of the pH effect on the optical properties of the calcium-morin system.

Morin (2-(2,4-dihydroxyphenyl)-3,5,7-trihydroxychromen-4-one) is an abundant flavonoid with various pharmacological and biological activities. Considering the ubiquitous presence of calcium cations in biological systems, it seems relevant to study the interaction of this ion with morin and the influence of pH on this system. In a first step, among the four hypothetical chelation sites, the preferential fixing site, its protonation state and the Ca environment have been determined by combining electronic spectroscopies and density functional theory (DFT) and time-dependent DFT calculations. Then, using the same methodology, the fate of the formed complex with the variation of pH was studied. Calcium chelation occurs with the 3-hydroxy-4-keto site with deprotonation of the hydroxyl group. The coordination number of CaII does not seem to be a determining parameter insofar whatever the number of solvent molecules present in the coordination sphere of the metal, the calculation of the electronic transitions leads to the same results. With the increase in pH, a first deprotonation of the complex occurs at the level of a solvent molecule in the metal coordination sphere, followed by a deprotonation of the hydroxyl function in position 7.

Natural organic matter-cations complexation and its impact on water treatment: A critical review.

The quality and quantity of natural organic matter (NOM) has been observed to evolve which poses challenges to water treatment facilities. Even though NOM may not be toxic itself, its presence in water has aesthetic effects, enhances biological growth in distribution networks, binds with pollutants and controls the bioavailability of trace metals. Even though NOM has heterogeneous functional groups, the predominant ones are the carboxyl and the phenolic groups, which have high affinities for metals depending on the pH. The properties of both the NOM and the trace elements influence the binding kinetics and preferences. Ca2+ prefers to bind with the carboxylic groups especially at a low pH while Zn2+ prefers the amine groups though practically, most cations bind to several functions groups. The nature of the chemical environment (neighboring ligands) the ligand finds itself equally influences its preference for a cation. The presence of NOM, cations or a complex of NOM-cations may have significant impact on the efficiency of water processes such as coagulation, adsorption, ion exchange resin and membrane filtration. In coagulation, the complexation between the coagulant salts and NOM helps to remove NOM from solution. This positive influence can further be enhanced by the addition of Ca2+. A negative influence is however, observed in lime-softening method as NOM complexes with Ca2+. A negative influence is also seen in membrane filtration where divalent cations partially neutralize the carboxyl functional groups of NOM thereby reducing the repulsion effect on NOM and increasing membrane fouling. The formation of disinfection by-products could either be increased or reduced during chlorination, the speciation of products formed is modified with generally the enhancement of haloacetic acid formation observed in presence of metal cations. This current work, presents in details the interactions of cations and NOM in the environment, the preference of cations for each functional group and the possible competition between cations for binding sites, as well as the possible impacts of the presence of cations, NOM, or their complex on water treatment processes.

Understanding the impact of the changes in weather conditions on surface water quality.

The aim of this paper is to better understand the functioning of the River Selle (northern France) during dry weather and storm events, to assess the impact of a town on the surface water quality and to suggest qualitative assumptions on the vulnerability of water quality to weather conditions. Two high-frequency monitoring stations covering the Cateau-Cambrésis town were deployed during 4 months in 2016. River flow, water temperature, pH, dissolved oxygen, turbidity, conductivity, total organic carbon, nitrates and phosphates were monitored every 10 min. The water supply of the River Selle is mainly dominated by groundwater as shown by the behaviour of the river flow, the water temperature and the nitrate concentrations in both surface water and groundwater. The reference station located at the upstream of the river (Saint Souplet) exhibits low anthropogenic pressure during dry weather but is significantly impacted during storm events. At the downstream of the Cateau-Cambrésis town, the water quality is severely impacted by phosphates during dry weather mainly due to wastewater inputs into the river. An additional load of pollution is highlighted during storm events. According to our results, the water quality of the River Selle would degrade if actions to reduce dry-weather and storm events pollution sources are not undertaken rapidly. Moreover, nutrients, particularly phosphates, are clearly in excess in this system. Efforts to combat soil leaching and the revision of sewage systems and urban wastewater treatment in the catchment are two key points to tackle. Finally, this study shows the importance of understanding the current behaviour of a given river towards dry weather and storm events before suggesting local scenarios of the impact of climate change on surface water quality.

Electronic Spectroscopies Combined with Quantum Chemistry Calculations: Study of the Interactions of 3-Hydroxyflavone with Copper Ions.

The current study aims at obtaining a better understanding of the mechanisms involved in the complexation of copper ions by 3-hydroxyflavone (3HF), which is one of the most studied compounds of the flavonoid family. To achieve this goal, quantum chemistry calculations combined with electronic spectroscopies, including absorption, fluorescence emission, and excitation, have been used. The formation of successive complexes of stoichiometry (metal/ligand) 1:2, 1:1, and 3:2 has been highlighted. Even under acidic conditions (pH = 4.0), the α-hydroxy-keto function of the molecule presents a high complexing power with regard to copper ions, insofar as a stable complex of 1:2 stoichiometry is obtained with a large conditional stability constant (log ß = 8.7). The formation of this predominant species induces a quenching of the dual fluorescence of 3HF, whereas the second complex of stoichiometry 1:1 presents a fluorescence emission.

Binding Specificity of Native Odorant-Binding Protein Isoforms Is Driven by Phosphorylation and O-N-Acetylglucosaminylation in the Pig Sus scrofa.

Odorant-binding proteins (OBP) are secreted in the nasal mucus at the vicinity of olfactory receptors (ORs). They act, at least, as an interface between hydrophobic and volatile odorant molecules and the hydrophilic medium bathing the ORs. They have also been hypothesized to be part of the molecular coding of odors and pheromones, by forming specific complexes with odorant molecules that could ultimately stimulate ORs to trigger the olfactory transduction cascade. In a previous study, we have evidenced that pig olfactory secretome was composed of numerous olfactory binding protein isoforms, generated by O-GlcNAcylation and phosphorylation. In addition, we have shown that recombinant OBP (stricto sensu) produced in yeast is made up of a mixture of isoforms that differ in their phosphorylation pattern, which in turn determines binding specificity. Taking advantage of the high amount of OBP secreted by a single animal, we performed a similar study, under exactly the same experimental conditions, on native isoforms isolated from pig, Sus scrofa, nasal tissue. Four fractions were obtained by using strong anion exchange HPLC. Mapping of phosphorylation and O-GlcNAcylation sites by CID-nanoLC-MS/MS allowed unambiguous localization of phosphosites at S13 and T122 and HexNAc sites at S13 and S19. T112 or T115 could also be phosphorylated. BEMAD analysis suggested extra phosphosites located at S23, S24, S41, S49, S57, S67, and T71. Due to the very low stoichiometry of GlcNAc-peptides and phosphopeptides, these sites were identified on total mixture of OBP isoforms instead of HPLC-purified OBP isoforms. Nevertheless, binding properties of native OBP isoforms to specific ligands in S. scrofa were monitored by fluorescence spectroscopy. Recombinant phosphorylated OBP-Pichia isoforms bind steroids and fatty acids with slight differences. Native isoforms, that are phosphorylated but also O-GlcNAcylated show radically different binding affinities for the same compounds, which strongly suggests that O-GlcNAcylation increases the binding specificity of OBP isoforms. These findings extend the role of O-GlcNAc in regulating the function of proteins involved in many mechanisms of metabolic homeostasis, including extracellular signaling in olfaction. Data is available via ProteomeXChange with identifier PXD011371.

Chalcogen substitution: Effect of oxygen-by-sulfur exchange on structural and spectroscopic properties of flavonols.

Quantum chemical calculations using density functional theory have revealed that the substitution of the ketone group by a thioketone one doesn't significantly change the structure of 3-hydroxyflavone. Notably, the strong intramolecular hydrogen bond involving the hydroxyl function is preserved if the O atom is substituted by an S atom, but also by Se or Te atoms. However, fundamental modifications are observed in both absorption and emission electronic spectra upon substitution, particularly the non-fluorescent behavior of the flavothione. All these changes were explained by the optimizations of the different excited states carried out by time-dependent DFT method.

A quantum chemistry evaluation of the stereochemical activity of the lone pair in PbII complexes with sequestering ligands.

The stereochemical activity of the lone pair on PbII complexes is assessed using several theoretical methods, including structural analyses, computations of Fukui functions, natural bond orbitals, electron localization function, investigation of the electron density and of its laplacian. The attention is focused on four octadentate N-carbamoylmethyl-substituted tetraazamacrocycles of various ring sizes ranging from 8 to 14 atoms associated with the PbII cation. The theoretical study illustrates the geometrical constraints imposed by the ring structure which limits the spatial development of the lone pair but without fully preventing it. For a given coordination number, the lone pair activity is strongly correlated to the geometry of the ligand and in particular to the size of the cage that the ligand forms around the PbII cation. Some limitations of the theoretical tools used are also evidenced, among them the necessity to sample around a critical point instead of just analyzing its nature. In the case of the laplacian of the electron density, a visualization method is introduced to moderate the results based only on the nature of a critical point. These limitations should also be related to the difficulty to extend the lone pair concept for the heaviest atoms of the classification.

Conformational and structural studies of N-methylacetohydroxamic acid and of its mono- and bis-chelated uranium(VI) complexes.

The thermodynamics and kinetics of the cis/trans isomerism of N-methylacetohydroxamic acid (NMAH) and its conjugated base (NMA(-)) have been reinvestigated in aqueous media by (1)H NMR spectroscopy. Hindered rotation around the central C-N bond due to electronic delocalization becomes slow enough on the NMR time scale to observe both rotamers in equilibrium in D2O at room temperature. By properly assigning the methyl group resonances, evidence for the prevalence of the E over the Z form is unambiguously provided [K300=[E]/[Z]=2.86(2) and 9.63(5) for NMAH and NMA(-), respectively], closing thereby a long-lasting dispute about the most stable conformer. To that end, calculations of the chemical shifts by density functional theory (DFT), which accurately reproduced the experimental data, turned out to be a much more reliable method than the direct computation of the relative energy for each conformer. The Z ⇌ E interconversion dynamics was probed at 300 K in D2O by 2D exchange-correlated spectroscopy (EXSY), affording the associated rate constants [kZE=9.0(2) s(-1) and kEZ=3.14(5) s(-1) for NMAH, kZE=0.96(3) s(-1) and kEZ=0.10(2) s(-1) for NMA(-)] and activation barriers at 300 K [ΔG(≠)ZE=68.0 kJ mol(-1) and ΔG(≠)EZ=70.6 kJ mol(-1) for NMAH, ΔG(≠)ZE=73.6 kJ mol(-1) and ΔG(≠)EZ=79.2 kJ mol(-1) for NMA(-)]. For the first time, mono- and bis-chelated uranium(VI) complexes of NMA(-) have been isolated. Crystals of [UO2(NMA)(NO3)(H2O)2] and [UO2(NMA)2(H2O)] have been characterized by X-ray diffractometry, infrared and Raman spectroscopies.

The complexation of AlIII, PbII, and CuII metal ions by esculetin: a spectroscopic and theoretical approach.

UV-visible absorption spectroscopy combined with quantum chemical calculations and, notably, Time-Dependent Density Functional Theory were used to probe the structure of metal complexes with esculetin in dilute aqueous solution, at pH = 5. For the 1:1 complex formation, the studied metal ions can be classified according to their complexing power: aluminum(III) > copper(II) > lead(II). For the three complexes, a chelate is formed with the fully deprotonated catechol moiety and an absorption band is observed at the same wavelength. In all cases, a pronounced ionic character is calculated for metal-ligand bonds. However, the complexes differ in their coordination sphere. Copper and lead are bound to two water molecules leading to a square plane geometry and a hemidirected complex, respectively, whereas aluminum atom has an octahedral environment involving three water molecules and a hydroxide ion. For Al(III) only, a 2:1 complex is observed, and the involvement of an aluminum dimer was evidenced.

pH influence on the complexation site of Al(III) with protocatechuic acid. A spectroscopic and theoretical approach.

Electronic spectroscopy techniques with the aid of quantum chemical calculations, and notably the Time-Dependent Density Functional Theory, can be used to probe the structure of metal complexes in solution. Here, we report the characterization of Al(III)-protocatechuate in aqueous solution, at pH=6.5. The exploitation of the UV-vis spectra of the system by chemometric methods highlights the formation of a single complex of stoichiometry 1:1. From different structural hypothesis, the comparison of theoretical and experimental spectra shows that Al(III) forms a monodentate complex with the carboxylate function. This hypothesis is confirmed by the calculation of the complexation reaction pathways. Previous studies report the formation of a chelate involving the ortho-dihydroxyl group, at pH=3.5. These results illustrate the important dependence of the protonation state of the carboxylic function on the Al(III) fixation site on the studied ligand.

Enhancement of the water solubility of flavone glycosides by disruption of molecular planarity of the aglycone moiety.

Enhancement of the water solubility by disruption of molecular planarity has recently been reviewed as a feasible approach in small-molecule drug discovery programs. We applied this strategy to some natural flavone glycosides, especially diosmin, a highly insoluble citroflavonoid prescribed as an oral phlebotropic drug. Disruption of planarity at the aglycone moiety by 3-bromination or chlorination afforded 3-bromo- and 3-chlorodiosmin, displaying a dramatic solubility increase compared with the parent compound.

Protic equilibria as the key factor of quercetin emission in solution. Relevance to biochemical and analytical studies.

A detailed spectrofluorimetric study on quercetin in aqueous solution proves that its anionic forms are responsible for a strong fluorescence enhancement observed at pH > 6. Anion fluorescence is also observed in organic solvents with strong hydrogen bond acceptor properties. The results provide a new interpretation of biophysical and analytical literature data where the fluorescence of the anionic forms of quercetin has never been explicitly taken into account. In particular, comparison with published binding studies strongly suggests that quercetin deprotonation and consequent fluorescence enhancement takes place when the flavonoid binds to several biological macromolecules. This observation can be very helpful in the understanding at a molecular level of the interaction between quercetin and the biomolecule.

Binding specificity of recombinant odorant-binding protein isoforms is driven by phosphorylation.

Native porcine odorant-binding protein (OBP) bears eleven sites of phosphorylation, which are not always occupied in the molecular population, suggesting that different isoforms could co-exist in animal tissues. As phosphorylation is a dynamic process resulting in temporary conformational changes that regulate the function of target proteins, we investigated the possibility that OBP isoforms could display different binding affinities to biologically relevant ligands. The availability of recombinant proteins is of particular interest for the study of protein/ligand structure-function relationships, but prokaryotic expression systems do not perform eukaryotic post-translational modifications. To investigate the role of phosphorylation in the binding capacities of OBP isoforms, we produced recombinant porcine OBP in two eukaryotic systems, the yeast, Pichia pastoris, and the mammalian CHO cell line. Isoforms were separated by anion exchange HPLC, and their phosphorylation sites were mapped by MALDI-TOF mass spectrometry and compared to those of the native protein. Binding experiments with ligands of biological relevance in the pig, Sus scrofa, were performed by fluorescence spectroscopy on two isoforms of recombinant OBP expressed in the yeast. The two isoforms, differing only by their phosphorylation pattern, displayed different binding properties, suggesting that binding specificity is driven by phosphorylation.

Phenylalanine 35 and tyrosine 82 are involved in the uptake and release of ligand by porcine odorant-binding protein.

Structural and molecular dynamics studies have pointed out the role of aromatic residues in the uptake of ligand by porcine odorant-binding protein (pOBP). The shift of Tyr82 from its position during the opening of the binding cavity has been shown, and was supposed to participate in the entrance of the ligand. Several Phe residues in the vicinity of Tyr82 could also participate in the binding process. To clarify their involvement, we performed molecular dynamics studies to simulate the dissociation of undecanal, a ligand previously co-crystallized with pOBP. The results confirmed the key-role of Tyr82 and pointed out the participation of Phe35 in controlling the reorientation of undecanal towards the exit. To bring experimental support to both published (binding) and present simulations (dissociation), we have mutated these two residues and over expressed the wild type pOBP, the two single mutants and the double mutant in the yeast Pichia pastoris. As fluorescence spectroscopy implies the uptake of the fluorescent probe and release in displacement experiments, we monitored the binding ability of the four proteins for 1-aminoanthracene (1-AMA). The experimental results indicated that both residues are involved in the uptake of ligand as the three mutated proteins were unable to bind 1-AMA, contrary to the wild type recombinant pOBP that bound 1-AMA with the expected affinity.

Complexation of lead(II) by chlorogenic acid: experimental and theoretical study.

Density functional theory (DFT) structure calculations and time-dependent DFT electronic excitation calculations have been performed on chlorogenic acid (H(3)CGA), a polyphenolic compound, used as a model molecule of humic substances. The different deprotonated forms of H(3)CGA have also been investigated. H(3)CGA is a multisite ligand that presents several metal complexing sites in competition, notably the carboxylic and catechol moieties. In low acidic aqueous medium, the complexation of Pb(II) has been followed by electronic absorption spectrometry. The formation of two complexes of stoichiometry metal:ligand 1:1 (log beta(1:1) = 3.39) and 2:1 (log beta(2:1) = 7.12) has been highlighted with use of chemometric methods. The theoretical spectrum of the 1:1 complex obtained by TD-DFT methodology shows the formation of a chelate [Pb(H(2)CGA)(H(2)O)(3)](+) with the metal fixation at the level of the carboxylate function. The second complexing site, the catechol moiety, is rapidly involved in the formation of the 2:1 complex from molar ratios [metal]/[ligand] higher than 0.1. The electronic transitions calculated for both free ligand and complexes involved the same molecular orbitals, and no ligand-metal or metal-ligand charge transfer is observed.

Toward a better understanding of the regioselectivity of the Al(III)-protocatechuic acid complexation reaction.

Protocatechuic acid presents two complexing sites in competition to fix metal: the carboxylic and catechol functions. Even in acidic aqueous medium, where the free ligand is fully protonated, Al(III) forms a chelate with the doubly deprotonated catechol group. To gain a better understanding of the complexation mechanism and to explain the regioselectivity of the reaction, reaction pathways involving either the catechol group or the carboxylic one have been calculated at the B3LYP/6-31G(d,p) level of theory. All the intermediate species have been identified, and both processes present the following different steps: metal attack with the coordination of Al(III) to an oxygen atom; deprotonation of hydroxyl groups; ring closure to form a chelate. Whatever the complexing site, a bidentate complex is more stable than a monodentate one. From an energetic point of view, the reaction pathway corresponding to a chelate formation with the catechol function is favored; notably the energy barrier necessary to close the ring involving the metal ion is calculated to be lower than that of carboxyl function.

Photochemistry of metal complexes of 3-hydroxyflavone: towards a better understanding of the influence of solar light on the metal-soil organic matter interactions.

The photo-stability of 3-hydroxyflavone (3HF) and its complexes with Al(iii), Zn(ii) and Pb(ii) in methanol was investigated by a multi-disciplinary strategy, combining UV-Vis, fluorescence, Raman and FT-IR spectroscopies, DFT and time-dependent DFT calculations and a traditional organic photochemistry approach. We found that the presence of metals can slow down (in the case of Pb(ii)) or even block (in the case of Al(iii)) the photo-degradation of 3HF. The Zn(ii) complex shows a reactivity comparable to free 3HF. In all cases (except the Al(iii) complex) the photo-product is 3-hydroxy-3-phenyl-1,2-indandione, the same as reported in literature for 3HF photochemistry in methanol. This means that metallic cations do not modify the photochemical mechanism of the reaction. In addition, in the case of Zn(ii) and Pb(ii) complexes, the photo-produced 3-hydroxy-3-phenyl-1,2-indandione was found to exist in free form, i.e. without metal complexation. This means that similar photo-reactions occurring in soil organic matter under solar irradiation entail desorption of free Zn(2+) and Pb(2+) cations (the most toxic form) in the environment. The presence of external parameters-presence of water and oxygen-has also been studied. Interestingly, opposite effects have been found for free 3HF and Zn(ii) and Pb(ii) complexes. Tentative explanations for these effects are provided, relying on a detailed investigation on the structure and on the photophysical properties of the three complexes.