Pentacoordinate Species Research Articles

Resolving intermediates during the growth of aluminum deuteroxide (Hydroxide) polymorphs in high chemical potential solutions

Aluminum hydroxide polymorphs are of widespread importance yet their kinetics of nucleation and growth remain beyond the reach of current models. Here we attempt to unveil the reaction processes underlying the polymorphs formation at high chemical potential. We examine their formation in-situ from supersaturated alkaline sodium aluminate solutions using deuteration and time-resolved neutron pair distribution function analyses, which indicate the formation of individual Al(OD)3 layers as an intermediate particle phase. These layers ultimately stack to form gibbsite- or bayerite-like layered heterostructures. Ex-situ characterization of the recovered precipitates using 27Al magic angle spinning nuclear magnetic resonance spectroscopy, Raman, X-ray diffraction, and scanning electron microscopy, suggests the presence of additional intermediate states, an amorphous compound bearing both tetrahededrally- and penta-coordinated Al3+. These observations reveal the complex pathways to form Al(OD)3 monolayers via either transient pentacoordinate species or amorphous-to-ordered transitions. The subsequent crystallization of admixed gibbsite/bayerite is followed by an Al(OD)3 monolayer attachment process.

Diorganotin (IV) amino acid complexes as potential anticancer agents. Synthesis, structural characterization, and in vitro assays

Nine new organotin (IV) derivatives from L-amino acids (l-lysine, L-ornithine, L-glutamic acid, and L-aspartic acid) were synthesized by one-pot ultrasound-assisted methodology. All compounds were characterized by ATR-FTIR (Attenuated Total Reflectance-Fourier Transform Infrared), LRMS (Low-Resolution Mass Spectrometry), and solution NMR (1H, 13C, 119Sn Nuclear Magnetic Resonance) spectroscopies. Complexes Bu2Sn(Lys) (1), Ph2Sn(Lys) (2), Bu2Sn(Orn) (3), and Ph2Sn (Glu-OMe) (6a) were crystallized, and the structures were established by single-crystal X-ray diffraction analysis. Diffraction results evidenced that complexes 1 to 3 were five-coordinated mononuclear species while the phenyl substituted derivative Ph2Sn (Glu-OMe) (6a) forms a polymeric network via Sn–O–Sn bridging whereby the tin atom is six-coordinated. In turn, 119Sn NMR results revealed that all tin complexes exist as mononuclear penta-coordinated species in solution. The tin derivatives were screened for ADME (Adsorption, Distribution, Metabolism, and Excretion) properties via the freely available tools SWISS ADME, and the results were analyzed hereafter. The antiproliferative activity of the complexes was tested against three human cancer cell lines: colorectal adenocarcinoma HT-29, breast adenocarcinoma MDA-MB-231, and chondrosarcoma SW-1353 using a non-tumoral cell line of human osteoblast as control, demonstrating selective inhibitory activities against cancer cells. Hence, these compounds could be a promising alternative to classical chemotherapy agents.

Co(II) Substitution Enhances the Esterase Activity of a de Novo Designed Zn(II) Carbonic Anhydrase.

Carbonic Anhydrases (CAs) have been a target for de novo protein designers due to the simplicity of the active site and rapid rate of the reaction. The first reported mimic contained a Zn(II) bound to three histidine imidazole nitrogens and an exogenous water molecule, hence closely mimicking the native enzymes' first coordination sphere. Co(II) has served as an alternative metal to interrogate CAs due to its d7 electronic configuration for more detailed solution characterization. We present here the Co(II) substituted [Co(II)(H2O/OH-)]N(TRIL2WL23H)3 n+ that behaves similarly to native Co(II) substituted human-CAs. Like the Zn(II) analogue, the cobalt-derivative at slightly basic pH is incapable of hydrolyzing p-nitrophenylacetate (pNPA); however, as the pH is increased a significant activity develops, which at pH values above 10 eventually yields a catalytic efficiency that exceeds that of the [Zn(II)(OH-)]N(TRIL2WL23H)3 + peptide complex. X-ray absorption analysis is consistent with an octahedral species at pH 7.5 that converts to a 5-coordinate species by pH 11. UV-vis spectroscopy can monitor this transition, giving a pKa for the conversion of 10.3. We assign this conversion to the formation of a 5-coordinate Co(II)(Nimid)3(OH)(H2O) species. The pH dependent kinetic analysis indicates the maximal rate (kcat), and thus the catalytic efficiency (kcat/Km), follow the same pH profile as the spectroscopic conversion to the pentacoordinate species. This correlation suggests that the chemically irreversible ester hydrolysis corresponds to the rate determining process.

Mechanistic insights into nitric oxide generation from nitrite via O-atom transfer in the unsymmetrical β-diketiminato copper(II) nitrite complex.

In this study, we employed DFT calculations to elucidate the mechanism of NO generation from nitrite via PPh3-induced oxygen atom transfer (OAT) in the unsymmetrical β-diketiminato copper(II), LCuIIONO. We discovered that the OAT process involves the cooperation of two PPh3 ligands and follows the mechanism distinct from that of the symmetrical β-diketiminato analogue. The ΔG‡ value, calculated to be 34.8 kcal mol-1, closely matches experimental data. The finding is further supported by analyzing the OAT product yields with varying equivalents of PPh3. The penta-coordinated species 5a, with PPh3 occupying the axial site, forms in the final stage of the OAT process. The isomerization of 5a and the decoordination of the hemilabile pyridyl arm synergistically reduce Cu(II) to Cu(I), facilitating NO release from the Cu(I) centre. These computational results provide valuable insights for the ligand design for PPh3-induced OAT reactions to produce NO in Cu(II) nitrite systems.

A Dicationic fac-Re(bpy)(CO)3Cl for CO2 Electroreduction at a Reduced Overpotential.

A dicationic Re bipyridine-type complex, fac-Re(6,6'-(2-((trimethylammonio)-methyl)phenyl)-2,2'-bipyridine )(CO)3Cl hexafluorophosphate (12+), has been synthesized, and its electrochemical behavior under Ar and CO2 has been investigated. The presence of pendent tetra-alkylammonium cations induces an anodic shift in the electrocatalytic potential for CO2 reduction relative to structurally similar model complexes. The electrochemical mechanisms in anhydrous CH3CN and in the presence of weak acids (water or trifluoroethanol) have been analyzed using cyclic voltammetry assisted by infrared spectroelectrochemistry and theoretical calculations. The dication enables catalysis at a diminished potential through Coulombic stabilization of the doubly reduced pentacoordinate species, its CO2 adduct, the hydroxide anion, and the conjugate base formed during acid-assisted C-OH bond cleavage of the metallocarboxylic acid to the metallocarbonyl and H2O. The major reduction product is CO, but in the presence of trifluoroethanol, formate is also produced with 14% Faradaic efficiency.

Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis

(1) Background: the theoretical modelling of reactions occurring in liquid phase is a research line of primary importance both in theoretical-computational chemistry and in the context of organic and biological chemistry. Here we present the modelling of the kinetics of the hydroxide-promoted hydrolysis of phosphoric diesters. (2) Method: the theoretical-computational procedure involves a hybrid quantum/classical approach based on the perturbed matrix method (PMM) in conjunction with molecular mechanics. (3) Results: the presented study reproduces the experimental data both in the rate constants and in the mechanistic aspects (C-O bond vs. O-P bond reactivity). The study suggests that the basic hydrolysis of phosphodiesters occurs through a concerted ANDN mechanism, with no formation of penta-coordinated species as reaction intermediates. (4) Conclusions: the presented approach, despite the approximations, is potentially applicable to a large number of bimolecular transformations in solution and therefore leads the way to a fast and general method to predict the rate constants and reactivities/selectivities in complex environments.

Dithiocarbazate based oxidomethoxidovanadium(V) and mixed-ligand oxidovanadium(IV) complexes: Study of solution behavior, DNA binding, and anticancer activity

In this work, one oxidomethoxidovanadium(V) [VVO(L)(OMe)] (1) and two mixed-ligand oxidovanadium(IV) [VIVO(L)(phen)] (2), and [VIVO(L)(bipy)] (3) complexes have been synthesized using a tridentate bi-negative ONS donor dithiocarbazate as main ligand, H2L [where, H2L = S-benzyl-3-(2-hydroxy-3-ethoxyphenyl)methylenedithiocarbazate] along with 1,10-phenanthroline (phen) (for 2) and 2,2′-bipyridine (bipy) (for 3) as co-ligands. The ligand and complexes have been characterised by FT-IR, UV–vis, NMR, and HR-ESI-MS techniques. Distorted square pyramidal for 1, and distorted octahedral geometry for 2 and 3 was confirmed by single crystal X-ray crystallography. The behavior of 1–3 in solution medium has been investigated through various physicochemical techniques. It is observed that 1 completely and 2–3 partially decomposes and converts into a penta-coordinated species, [VIVO(L)(DMSO/H2O)] after the release of the methoxido group (1) or breaking of the diimine based co-ligands (2 and 3) in DMSO/aqueous solution. Interestingly, in DMSO/aqueous solution, 1 gets completely reduced and converted into the corresponding oxidovanadium(IV) species. Interaction of 1–3 with calf thymus DNA (CT-DNA) was investigated and the results show, complex 2 exhibited the maximum binding constants, Kb = 7.12 × 104 M−1. The anticancer potential of 1–3 was evaluated by cell viability assay against human breast carcinoma cell, MCF-7, and noncancerous mouse embryonic cell, NIH-3T3 and 2 was found to be the most cytotoxic complex (IC50 = 6.73 ± 0.36 μM) in the series. In addition, 2 selectively inhibit colony formation compared to the rest complexes. Also, the cell cycle studies of the complexes were performed using flow cytometry analysis.

The Impact of 3-(trihydroxysilyl)-1-propanesulfonic Acid Treatment on the State of Vanadium Incorporated on SBA-15 Matrix

Bifunctional catalysts—e.g., those with acidic and redox sites—are of particular importance, especially in the cascade processes, including the one-pot transformation of glycerol to acrylic acid. In this study, we explore one aspect of the preparation of a vanadium-containing catalyst, which can be further modified with 3-(trihydroxysilyl)-1-propanesulfonic acid (TPS). The state of vanadium species loaded on mesoporous ordered silica of SBA-15 type was investigated before and after treatment with TPS, which can also be applied for the generation of acidic centers. Two vanadium sources, i.e., ammonium metavanadate and vanadium(IV) oxide sulfate, were applied to generate redox sites on SBA-15. The structure of materials obtained was analyzed using N2 adsorption/desorption and XRD measurements. For the estimation of the amount of vanadium and characterization of its state, the following techniques were applied: ICP, UV-Vis, XPS, ESR and FTIR combined with pyridine adsorption. The treatment of vanadium containing SBA-15 with TPS was found to lead to the oxidation of V4+ to V5+ and the partial removal of vanadium species, leading to a decrease in the number of penta-coordinated vanadium species. These features should be taken into account in the design of bifunctional catalysts with vanadium-active centers and SO3H acidic sites coming from TPS.

Unusually Fast bis-Histidyl Coordination in a Plant Hemoglobin.

The recently identified nonsymbiotic hemoglobin gene MtGlb1-2 of the legume Medicago truncatula possesses unique properties as it generates four alternative splice forms encoding proteins with one or two heme domains. Here we investigate the ligand binding kinetics of MtGlb1-2.1 and MtGlb1-2.4, bearing two hemes and one heme, respectively. Unexpectedly, the overall time-course of ligand rebinding was unusually fast. Thus, we complemented nanosecond laser flash photolysis kinetics with data collected with a hybrid femtosecond–nanosecond pump–probe setup. Most photodissociated ligands are rebound geminately within a few nanoseconds, which leads to rates of the bimolecular rebinding to pentacoordinate species in the 108 M−1s−1 range. Binding of the distal histidine to the heme competes with CO rebinding with extremely high rates (kh ~ 105 s−1). Histidine dissociation from the heme occurs with comparable rates, thus resulting in moderate equilibrium binding constants (KH ~ 1). The rate constants for ligation and deligation of distal histidine to the heme are the highest reported for any plant or vertebrate globin. The combination of microscopic rates results in unusually high overall ligand binding rate constants, a fact that contributes to explaining at the mechanistic level the extremely high reactivity of these proteins toward the physiological ligands oxygen, nitric oxide and nitrite.

Group 14 atoms - plane and simple.

Silicon and germanium are predicted to form stable planar pentacoordinate species when inside a ring of five donor atoms.

The role of different network modifying cations on the speciation of the Co2 + complex in silicates and implication in the investigation of historical glasses

In the last decades the speciation of the cobalt complex in a glass matrix has been extensively studied. Bivalent cobalt ions in glasses of different composition commonly adopt a tetrahedral coordination, though hexa- or penta-coordinated species are also possible. Changes in the absorbance spectrum of Co-doped glasses were attested in previous studies according to the introduction of different modifying cations. A shifting of the first sub-band characterizing the typical triplets of tetrahedral Co2+ ions in both the visible and near infrared regions was observed, but discrepancies in literature suggested a relevant role of glass composition on the definition of the optical signature of cobalt. Co-doped glasses with different composition (soda-lime, potash-lime, mixed alkali and ZnO-Na2O-CaO-SiO2) were studied via Fiber Optic Reflectance Spectroscopy (FORS). Pseudo-Voigt functions were used for the deconvolution of the absorbance spectra and the features of the bands characteristic of each cobalt complex were investigated. The structural role played by each modifying cation and the fundamental implications of glass basicity on the speciation of different Co-complexes were stressed. Changes in glass structure resulted in different equilibria between the three absorbing species whose specific optical signatures in the 480–530nm region interact to determine the resulting absorbance spectrum.

Theoretical illumination of highly original photoreactive 3MC states and the mechanism of the photochemistry of Ru(ii) tris(bidentate) complexes.

We have identified highly novel photoreactive 3MC states of ruthenium(ii) 4,4'-bi-1,2,3-triazolyl (btz) complexes of the form [Ru(N^N)(btz)2]2+ and have elucidated the mechanism of the highly unusual experimental observations of photochemical ligand dechelation and concomitant ligand rearrangement reactivity to form unusual photoproducts trans-[Ru(N^N)(κ2-btz)(κ1-btz)(solvent)]2+. The triplet metal-to-ligand charge-transfer (3MLCT) states and classical Jahn-Teller type triplet metal-centred (3MC) states of the series of complexes [Ru(N^N)3-n(btz)n]2+ (btz = 4,4'-bi-1,2,3-triazolyl; N^N = 2,2'-bipyridyl (bpy), n = 0 (1), 1 (2), 2 (3), 3 (5); N^N = 4-(pyrid-2-yl)-1,2,3-triazole (pytz), n = 1 (4)) have been optimised by density functional theory (DFT) and characterised. There is a gradual and significant destabilisation of the 3MLCT states as the triazole content of the complexes increases, which occurs with a slight stabilisation of the 3MC states. Whilst consistent with the promotion of photochemical reactivity in the heteroleptic complexes of the series relative to 1, these classical 3MC states fail to account for the extraordinary ligand rearrangement processes that accompany ligand ejection. Thorough theoretical exploration of the lowest excited triplet potential energy surface (3PES) here reveals the existence of a new type of 3MC state and the role it plays in the photochemical reactivity of the complexes. This newly discovered state, called MC(F), displays a flattened geometry (indicated by the 'F' in the parentheses) which makes it clearly on the path to achieving the coplanarity of the bidentate ligands in the experimentally observed trans-photoproduct. Further novel 'pentacoordinate' 3MC states with coplanar bidentate ligands, called MC(P) (where the 'P' in the parentheses denotes the pentacoordinate character), were then identified and optimised. The energy barriers between the different triplet states were confirmed to be small which makes all triplet states accessible. Solvent trapping, which occurs on the singlet PES according to Wigner's rules, is finally achieved by a singlet pentacoordinate species to yield the monosolvento photoproduct. Thus, our calculations not only reveal highly novel 3MC states but more significantly demonstrate their crucial role in the formation of the experimentally observed photoproducts.

Conformational status of cytochrome c upon N-homocysteinylation: Implications to cytochrome c release

One of the proposed mechanisms of homocysteine (Hcy) toxicity is the post-translational modification of proteins by its metabolite, homocysteine thiolactone (HTL). Incubation of proteins with HTL has been shown to form covalent adducts with ε-amino group of lysine residues of protein (called N-homocysteinylation) which ultimately results in structural and functional alterations of the modified proteins. In the present study, the effects of HTL on the conformational and heme status of cytochrome c (cyt c) were investigated. Spectroscopic analyses revealed that HTL-modified cyt c undergoes certain conformational alterations leading to disturbed heme-Trp distance and packing of the apolar groups. These alterations were accompanied with the reduction of the heme moiety and activation of peroxidase-like function of cyt c, which is known to be a crucial event for initiation of the intrinsic apoptotic pathway. Further structural characterization revealed that disruption of the heme-Met80 interaction, thereby converting the hexa-coordinate cyt c to a penta-coordinate species (with a free heme ligand), was responsible for the activation of the peroxidase activity. The study provides insights for the possible role of cyt c N-homocysteinylation in eliciting its toxicity and cell death.

Deciphering the Conformational Choreography of Zinc Coordination Complexes with Standard and Novel Proton NMR Techniques Combined with DFT Methods.

The presence of water has been shown to deeply impact the stability and geometry of Zn complexes in solution. Evidence for tetra- and penta-coordinated species in a pyridylmethylamine-Zn(II) model complex is presented. Novel (1) H NMR tools such as T1 -filtered selective exchange spectroscopy and pure shifted gradient-encoded selective refocusing as well as classical 2D ((1) H-(1) H) exchange spectroscopy, diffusion-ordered spectroscopy and T1 ((1) H) measurements, in combination with density functional theory methods allow the full conformational dynamics of a pyridylmethylamine-Zn(II) complex to be revealed. Four conformers and two families of complexes depending on the hydration states are elucidated.

Aminomethylation Reaction of ortho-Pyridyl C–H Bonds Catalyzed by Group 3 Metal Triamido Complexes

Tris[N,N-bis(trimethylsilyl)amido] complexes of group 3 metals, especially yttrium and gadolinium, served as catalysts for ortho-C-H bond addition of pyridine derivatives and N-heteroaromatics into the C═N double bond of nonactivated imines to afford the corresponding aminomethylated products. Addition of catalytic amounts of secondary amines, such as dibenzylamine, dramatically improved the catalytic activity through the formation of a mixed ligated complex such as [(Me3Si)2N]2Y(NBn2)(THF) (4). Furthermore, kinetic studies using the isolated complex 4 provided a plausible reaction mechanism by which coordination of two pyridine derivatives afforded a penta-coordinated species as a key step.

A Fast Catalytic Process of Transfer of a Phosphorus Atom: How Folding of the Reagent is Related to its Catalytic Activity. A Possible Correlation with Rna Behavior

A simple and very fast process of transfer of a phosphorus atom, performed by a simple molecule acting as catalyst in an almost infinite catalytic cycle is described. The catalyst donates a P atom to a mixture of two different Grignard reagents giving, in a very fast and in a highly selective manner, only one phosphorus-containing compound with an enormous rate enhancement with respect to the corresponding no-catalyzed reaction which gives a final cluttered mixture of many organophosphorus products. The focal factor to explain this highly selective process of P transport lies in the folded structure of the reagent with particular angles around the phosphorus atom which can facilitate the formation of cyclic trigonal bipyramidal pentacoordinated species and then its catalytic activity. In a similar manner, RNA can adopt, in a precise position, a particular three-dimensional structure that might facilitate the formation of pentacoordinated species leading to the catalytic function.

Properties of ThFx from Infrared Spectra in Solid Argon and Neon with Supporting Electronic Structure and Thermochemical Calculations

Laser-ablated Th atoms react with F2 in condensing noble gases to give ThF4 as the major product. Weaker higher frequency infrared absorptions at 567.2, 564.8 (576.1, 573.8) cm(-1), 575.1 (582.7) cm(-1) and 531.0, (537.4) cm(-1) in solid argon (neon) are assigned to the ThF, ThF2 and ThF3 molecules based on annealing and photolysis behavior and agreement with CCSD(T)/aug-cc-pVTZ vibrational frequency calculations. Bands at 528.4 cm(-1) and 460 cm(-1) with higher fluorine concentrations are assigned to the penta-coordinated species (ThF3)(F2) and ThF5(-). These bands shift to 544.2 and 464 cm(-1) in solid neon. The ThF5 molecule has the (ThF3)(F2) Cs structure and is essentially the unique [ThF3(+)][F2(-)] ion pair based on charge and spin density calculations. Electron capture by (ThF3)(F2) forms the trigonal bipyramidal ThF5(-) anion in a highly exothermic process. Extensive structure and frequency calculations were also done for thorium oxyfluorides and Th2F4,6,8 dimer species. The calculations provide the ionization potentials, electron affinities, fluoride affinities, Th-F bond dissociation energies, and the energies to bind F2 and F2(-) to a cluster as well as dimerization energies.

Selective X-ray-induced NO photodissociation in haemoglobin crystals: evidence from a Raman-assisted crystallographic study

Despite their high physiological relevance, haemoglobin crystal structures with NO bound to haem constitute less than 1% of the total ligated haemoglobins (Hbs) deposited in the Protein Data Bank. The major difficulty in obtaining NO-ligated Hbs is most likely to be related to the oxidative denitrosylation caused by the high reactivity of the nitrosylated species with O(2). Here, using Raman-assisted X-ray crystallography, it is shown that under X-ray exposure (at four different radiation doses) crystals of nitrosylated haemoglobin from Trematomus bernacchii undergo a transition, mainly in the β chains, that generates a pentacoordinate species owing to photodissociation of the Fe-NO bond. These data provide a physical explanation for the low number of nitrosylated Hb structures available in the literature.

Bioactive Penta-Coordinated Diorganotin(Iv) Complexes of Pyridoxalimine Schiff Bases

Diorganotin(IV) complexes of an extended system derived from the condensation of pyridoxal hydrochloride with 2-amino phenol (H2L1), 2-amino-4-methyl phenol (H2L2), 2-amino-4-chloro phenol (H2L3), 2-amino-4-nitro phenol (H2L4), 1-amino-2-naphthol hydrochloride (H2L5) have been synthesized by the reaction of dichlorodiorganotin(IV) in a 1:1 molar ratio with these ligands. Spectral studies (IR, 1H, 13C, 119Sn NMR) along with physical data evidenced the formation of penta-coordinated species with the ligands acting as tridentate (ONO) with oxygen occupying the axial positions, and nitrogen at one of the equatorial positions. The ligands and their organotin complexes have been evaluated for antimicrobial activity against phytopathogenic fungi Candida albicans and Aspergillus niger at 25 ± 1 °C and bacteria Bacillus subtilis, Escherichia coli, and Staphylococcus aureus at 37 ± 1 °C. The activities of the ligands have been enhanced on complexation and the results indicate that they exhibit significant antimicrobial properties. Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.

Interplay between Cationic and Neutral Species in the Rhodium‐Catalyzed Hydroaminomethylation Reaction

The reactivity of [Rh(CO)(2){(R,R)-Ph-BPE}]BF(4) (2) toward amine, CO and/or H(2) was examined by high-pressure NMR and IR spectroscopy. The two cationic pentacoordinated species [Rh(CO)(3) {(R,R)-Ph-BPE}]BF(4) (4) and [Rh(CO)(2)(NHC(5)H(10)){(R,R)-Ph-BPE}]BF(4) (8) were identified. The transformation of 2 into the neutral complex [RhH(CO)(2){(R,R)-Ph-BPE}] (3) under hydroaminomethylation conditions (CO/H(2), amine) was investigated. The full mechanisms related to the formation of 3, 4 and 8 starting from 2 are supported by DFT calculations. In particular, the pathway from 2 to 3 revealed the deprotonation by the amine of the dihydride species [Rh(H)(2)(CO)(2){(R,R)-Ph-BPE}]BF(4) (6), resulting from the oxidative addition of H(2) on 2.