Apical Water Molecule Research Articles

Synthesis, crystal structure, Hirshfeld surface, and DFT studies of a Copper(II) complex of 5,5′-dimethyl-2,2′-bipyridine and 1,2,2-trimethylcyclopentane-1,3-dicarboxylic acid

A new metal-organic hybrid complex [Cu(5,5′-dmbipy) (D-cam) (H2O)]n (1), (5,5′-dmbipy = 5,5′-dimethyl-2,2′-bipyridine, D-cam = D-camphoric acid anion) was hydrothermally synthesized. This complex was characterized by FTIR spectroscopy, TGA, and single-crystal X-ray diffraction. Crystallographic studies show that the title complex 1 crystallizes in an orthorhombic system with a P212121 space group with a = 06.9518(05) Ǻ, b = 13.5516(13) Ǻ, c = 22.6380(02)Ǻ; V = 2132.7(3) Ǻ3. The title CuII complex adopts a square pyramidal configuration. DFT study and Hirshfeld topology analysis of complex 1 was also done. The crystal achieves its three-dimensional structure and stability through polymeric chains having helical motifs of arrangement in between moieties and interconnected through hydrogen bonding interactions between the apical water molecule and non-coordinated oxygen atoms of the D-cam2- ligands. TGA, DFT calculations and Hirshfeld topology analysis revealed that the title complex 1 was stable.

Structure and Population of Complex Ionic Species in FeCl2 Aqueous Solution by X-ray Absorption Spectroscopy.

Technologies for mass production require cheap and abundant materials such as ferrous chloride (FeCl2). The literature survey shows the lack of experimental studies to validate theoretical conclusions related to the population of ionic Fe-species in the aqueous FeCl2 solution. Here, we present an in situ X-ray absorption study of the structure of the ionic species in the FeCl2 aqueous solution at different concentrations (1–4 molL−1) and temperatures (25–80 °C). We found that at low temperature and low FeCl2 concentration, the octahedral first coordination sphere around Fe is occupied by one Cl ion at a distance of 2.33 (±0.02) Å and five water molecules at a distance of 2.095 (±0.005) Å. The structure of the ionic complex gradually changes with an increase in temperature and/or concentration. The apical water molecule is substituted by a chlorine ion to yield a neutral Fe[Cl2(H2O)4]0. The observed substitutional mechanism is facilitated by the presence of the intramolecular hydrogen bonds as well as entropic reasons. The transition from the single charged Fe[Cl(H2O)5]+ to the neutral Fe[Cl2(H2O)4]0 causes a significant drop in the solution conductivity, which well correlates with the existing conductivity models.

Quasi-Isostructural Co(II) and Ni(II) Complexes with Mefenamato Ligand: Synthesis, Characterization, and Biological Activity.

Three metal complexes of mefenamato ligand 1 were synthesized: [Co2(mef)4(EtOH)2(H2O)4]: 2; [Co(mef)2(MeOH)4]∙2MeOH: 3; and [Ni(mef)2(MeOH)4]∙2MeOH: 4. Their compositions and properties were investigated by elemental analysis (EA), flame atomic absorption spectrometry (FAAS), Fourier-transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA). Crystal structures were determined by the single crystal X-ray diffraction technique. Additionally, their antioxidant and antimicrobial activity were established, thus proving good/moderate bioactivity against Gram-positive bacteria and yeasts. In the crystal structure of 2, an apical water molecule is shared between two adjacent cobalt(II) ions, resulting in the formation of a polymeric chain extending along the [100] direction. Meanwhile, structures 3 and 4 have strong intermolecular hydrogen bonds with diverse topologies that yield unique quasi-isostructural arrangements. The packing topology is reflected by the Hirshfeld surface analysis of intermolecular contacts.

Diaquatetra-kis(μ-3-meth-oxy-benzoato-κ2 O 1:O 1')dicopper(II).

The asymmetric unit of the binuclear title compound, [Cu2(C8H7O3)4(H2O)2], comprises two halves of diaquatetra-kis-(μ-3-meth-oxy-benzoato-κ2 O 1:O 1')dicopper(II) units. The paddle-wheel structure of each complex is completed by application of inversion symmetry, with the inversion centre situated at the midpoint between two CuII atoms in each dimer. The two CuII atoms of each centrosymmetric dimer are bridged by four 3-meth-oxy-benzoate anions resulting in Cu⋯Cu separations of 2.5961 (11) and 2.6060 (12) Å, respectively. The square-pyramidal coordination sphere of each CuII atom is completed by an apical water mol-ecule. Inter-molecular O-H⋯O hydrogen bonds of weak nature link the complexes into layers parallel to (100). The three-dimensional network structure is accomplished by C-H⋯O hydrogen bonds inter-linking adjacent layers.

A supramolecular polymeric chain in the cobalt(II) complex with diclofenac: synthesis, crystal structure, spectroscopic, thermal and antioxidant activity

A cobalt(II) complex with empirical formula [Co(dicl)2·(H2O)3]·MeOH (where dicl = diclofenac) was synthesized and characterized by elemental analysis, flame atomic absorption spectroscopy (FAAS), infrared spectroscopy (FTIR) and thermal decomposition techniques (TGA). The crystal structure of the complex was determined by single crystal X-ray diffraction technique. The compound crystallizes in the monoclinic space group I2/a. Apical water molecules link adjacent cobalt(II) ions forming polymeric chains along the crystal a axis. The thermal behavior of the complex was studied by TG/DTG/DTA, TG/MS and TG/FTIR methods under non-isothermal conditions in air. Upon heating [Co(dicl)2·(H2O)3]·MeOH decomposes progressively to metal oxides, which are the final products of pyrolysis. Furthermore, antioxidant activity of the complex was examined.

Covalency and magnetic anisotropy in lanthanide single molecule magnets: the DyDOTA archetype.

Lanthanide ions when complexed by polyamino-polycarboxylate chelators form a class of compounds of paramount importance in several research and technological areas, particularly in the fields of magnetic resonance and molecular magnetism. Indeed, the gadolinium derivative is one of the most employed contrast agents for magnetic resonance imaging while the dysprosium one belongs to a new generation of contrast agents for T2-weighted MRI. In molecular magnetism, Single Molecule Magnets (SMMs) containing lanthanide ions have become readily popular in the chemistry and physics communities since record energy barriers to the reversal of magnetization were reported. The success of lanthanide complexes lies in their large anisotropy due to the contribution of the unquenched orbital angular momentum. However, only a few efforts have been made so far to understand how the f-orbitals can be influenced by the surrounding ligands. The outcomes have been rationalized using mere electrostatic perturbation models. In the archetype compound [Na{Dy(DOTA) (H2O)}]·4H2O (Na{DyDOTA}·4H2O) an unexpected easy axis of magnetization perpendicular to the pseudo-tetragonal axis of the molecule was found. Interestingly, a dependency of the orientation of the principal magnetization axis on the simple rotation of the coordinating apical water molecule (AWM) - highly relevant for MRI contrast - around the Dy-OAWM bond was predicted by ab initio calculations, too. However, such a behaviour has been contested in a subsequent paper justifying their conclusions on pure electrostatic assumptions. In this paper, we want to shed some light on the nature of the subtle effects induced by the water molecule on the magnetic properties of the DyDOTA archetype complex. Therefore, we have critically reviewed the structural models already published in the literature along with new ones, showing how the easy axis orientation can dangerously depend on the chosen model. The different computed behaviors of the orientation of the easy axis of magnetization have been rationalized as a function of the energy gap between the ground and the first excited doublet. Magneto-structural correlations together with a mapping of the electrostatic potential generated by the ligands around the Dy(iii) ion through a multipolar expansion have also been used to evidence and quantify the covalent contribution of the AWM orbitals.

Syntheses, X-ray crystal structures and spectroscopic characterization of rare μ-di-σ pyrazole based bridging keto carbonyl complexes derived from Cd(II) salts

The pyrazole based ligands (E)-2-(3,5-dimethyl-1H-pyrazol-1-yl)-N′-(pyridin-2-ylmethylene acetohydrazide (N-PzOPyH) and (E)-5-methyl-N′-(pyridin-2-ylmethylene)-1H-pyrazole-3-carbo hydrazide (PzOPyH), a 1:1 condensation product of 2-(3,5-dimethyl-1H-pyrazol-1-yl)aceto hydrazide and 5-methylpyrazole-3-carbohydrazide with pyridine-2-carbaldehyde respectively, and their keto oxygen bridged Cd(II) complexes [Cd2(N-PzOPy)2(H2O)4](ClO4)4 (1), [Cd2(PzOPy)2(H2O)4](ClO4)4 (2) and [Cd2(PzOPy)2(NO3)4] (3)] are reported. They have been characterized structurally and spectroscopically. The potential tetradentate NONN-donor ligands N-PzOPyH and PzOPyH are engaged in the coordination around the cadmium(II) center through the nitrogen atoms of pyrazole, azomethine and pyridine and the ketonic oxygen atom of the carbohydrazide group to form complexes 1, 2 and 3, respectively. These ligands span themselves in the equatorial plane and the pentagonal bipyramidal geometry is completed around the metal centres (with an N3O4 chromophore) with two apical water molecules (for 1 and 2) and with two nitrate ions (for 3). These keto bridged Cd(II) complexes are further stabilised by supramolecular interactions, like π⋯π, C–H⋯π and H-bonding interactions.

Crystal structure of magnesium selenate hepta-hydrate, MgSeO4·7H2O, from neutron time-of-flight data.

MgSeO4·7H2O is isostructural with the analogous sulfate, MgSO4·7H2O, consisting of isolated [Mg(H2O)6](2+) octa-hedra and [SeO4](2-) tetra-hedra, linked by O-H⋯O hydrogen bonds, with a single inter-stitial lattice water mol-ecule. As in the sulfate, the [Mg(H2O)6](2+) coordination octa-hedron is elongated along one axis due to the tetra-hedral coordination of the two apical water mol-ecules; these have Mg-O distances of ∼2.10 Å, whereas the remaining four trigonally coordinated water mol-ecules have Mg-O distances of ∼2.05 Å. The mean Se-O bond length is 1.641 Å and is in excellent agreement with other selenates. The unit-cell volume of MgSeO4·7H2O at 10 K is 4.1% larger than that of the sulfate at 2 K, although this is not uniform; the greater part of the expansion is along the a axis of the crystal.

A new trinuclear zinc(II) complex and a heptacoordinated mononuclear cadmium(II) complex with a pyrimidine derived Schiff base ligand: Syntheses, crystal structures, photoluminescence and DFT calculations

The new N6 donor hexadentate Schiff base 2,4-bis [2-(pyridine-2-ylmethylidene) hydrazinyl] pyrimidine (L), its trinuclear Zn(II) complex, [Zn3(L)2Cl6] (1) and mononuclear heptacoordinate Cd(II) complex [Cd(L)(H2O)2](ClO4)2 (2) have been synthesised and characterised by crystallographically and spectroscopically. Complex 1 is featured by the triangular arrangement of three zinc atoms where the neighbouring Zn atoms are linked via half portion (N3 chromophore) of the same ligand molecule. In 1, the ligand molecules behave as hexadentate ones (employing both pyrimidine nitrogen atoms as active donor centres) to create the octahedral environment around Zn(II). The central and terminal Zn(II) atom has N6 and N3Cl3 chromophores respectively. In 2 the same ligand (L) behaves as pentadentate one (ignoring one pyrimidine nitrogen in the coordination process) to produce a pentagonal bipyramidal geometry with two apical water molecules. The geometries of both complexes were optimised in the singlet state by DFT method. The TDDFT calculations have been done on the optimised geometries to understand the electronic structure and spectral transition in the complexes. Complex 1 exhibits intraligand 1(π→π*) fluorescence in aqueous methanol solvent at room temperature.

Magnetic Anisotropy and Spin‐Parity Effect Along the Series of Lanthanide Complexes with DOTA

Spotting trends: Upon going from Tb(III) to Yb(III) centers in the complexes of the DOTA(4-) ligand, a reorientation of the easy axis of magnetization from perpendicular to parallel to the Ln-O bond of the apical water molecule is experimentally observed and theoretically predicted (SMM=single-molecule magnet). Only ions with an odd number of electrons show slow relaxation of the magnetization.

μ-4,4'-Bipyridine-bis-[aqua-(4-hy-droxy-pyridine-2,6-dicarboxyl-ato)copper(II)

The title compound, [Cu2(C7H3NO5)2(C10H8N2)(H2O)2], exhibits a centrosymmetric binuclear molecule. Each completely deprotonated 4-hy­droxy­pyridine-2,6-dicarb­oxy­lic acid mol­ecule assumes a tridentate chelating coordination mode. The square-pyramidal coordination geometry around the CuII ion is completed by the bridging bipyridine ligand and an apical water molecule. Adjacent complexes are connected via O—H⋯O and C—H⋯O hydrogen bonds to generate a three-dimensional supra­molecular structure.

Magnetic Anisotropy in a Dysprosium/DOTA Single‐Molecule Magnet: Beyond Simple Magneto‐Structural Correlations

Magnetic moments: The orientation of the title single-molecule magnet was investigated by magnetic single crystal and luminescence characterization, supported by ab initio calculations, and was found to be governed by the position of the hydrogen atoms of the apical water molecules. This finding suggests that simple magneto-structural correlations can give misleading clues for research in molecular magnetism as well as in the design of MRI contrast agents. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Structures of the Phosphorylated and VO3-Bound 2H-Phosphatase Domain of Sts-2

The C-terminal domain of the suppressor of T cell receptor (TCR) signaling 1 and 2 (Sts-1 and -2) proteins has homology to the 2H-phosphatase family of enzymes. The phosphatase activity of the correspondent Sts-1 domain, Sts-1(PGM), is key for its ability to negatively regulate the signaling of membrane-bound receptors including TCR and the epidermal growth factor receptor (EGFR). A nucleophilic histidine, which is transiently phosphorylated during the phosphatase reaction, is essential for the activity. Here, we present the crystal structure of Sts-2(PGM) in the phosphorylated active form and bound to VO(3), which represent structures of an intermediate and of a transition state analogue along the path of the dephosphorylation reaction. In the former structure, the proposed nucleophilic His366 is the only phoshorylated residue and is stabilized by several interactions with conserved basic residues within the active site. In the latter structure, the vanadium atom sits in the middle of a trigonal bipyramid formed by the three oxygen atoms of the VO(3) molecule, atom NE2 of His366, and an apical water molecule W(a). The V-NE2 bond length (2.25 A) suggests that VO(3) is not covalently attached to His366 and that the reaction mechanism is partially associative. The two structures also suggest a role for Glu476 in activating a uniquely positioned water molecule. In both structures, the conformation of the active site is remarkably similar to the one seen in apo-Sts-2(PGM) suggesting that the spatial arrangement of the catalytic residues does not change during the dephosphorylation reaction.

Structural changes induced by dehydration in the crystalline layered silicate Na-RUB-18: a computational/experimental combined study

Na-RUB-18 layered silicate (Na8Si32O64(OH)8·32H2O) is prepared following the procedure reported in the literature (: K. Kosuge and A. Tsunashima, J. Chem. Soc., Chem. Commun., 1995, 2427) and its significant structural modifications induced by progressive removal of hydration water molecules are studied for the first time by a combined experimental (TGA and variable temperature XRD and FTIR) and theoretical approach. A novel structure of a partially de-hydrated Na-RUB-18 obtained upon heating at 75 °C under inert gas flow, which leads to a reversible phase transformation in agreement with XRD and FTIR results, is found. TGA indicates that at this stage, two of the four hydration water molecules per Na ion are lost. Theoretical results based on DFT calculations suggest that the apical water molecules of the solvated octahedrally coordinated sodium ion, forming weak H-bonds with the silicate oxygen atoms, are removed at this stage. As a consequence of the dehydration, the silicate layers get closer, and, similarly to that observed for zeolites, the sodium ions move towards lattice oxygen atoms, to restore their coordination shell. A combination of IR spectroscopy and computational models is used to describe the vibrational properties of silanol/silanolate (SiOH⋯SiO)−1 bridges, which are responsible for the proton conduction of Na-RUB-18. The method described can be of general utility to refine structures which are not fully accessible to standard X-ray structure analysis.

Systematic Study of the Functions for the Residues around the Nucleotide Pocket in Simian Virus 40 AAA+ Hexameric Helicase

The high-resolution structural data for simian virus 40 large-T-antigen helicase revealed a set of nine residues bound to ATP/ADP directly or indirectly. The functional role of each of these residues in ATP hydrolysis and also the helicase function of this AAA+ (ATPases associated with various cellular activities) molecular motor are unclear. Here, we report our mutational analysis of each of these residues to examine their functionality in oligomerization, DNA binding, ATP hydrolysis, and double-stranded DNA (dsDNA) unwinding. All mutants were capable of oligomerization in the presence of ATP and could bind single-stranded DNA and dsDNA. ATP hydrolysis was substantially reduced for proteins with mutations of residues making direct contact with the gamma-phosphate of ATP or the apical water molecule. A potentially noncanonical "arginine finger" residue, K418, is critical for ATP hydrolysis and helicase function, suggesting a new type of arginine finger role by a lysine in the stabilization of the transition state during ATP hydrolysis. Interestingly, our mutational data suggest that the positive- and negative-charge interactions in the uniquely observed residue pairs, R498/D499 and R540/D502, in large-T-antigen helicase are critically involved in the transfer of energy of ATP binding/hydrolysis to DNA unwinding.

Crystal Structure of a Trapped Phosphate Intermediate in Vanadium Apochloroperoxidase Catalyzing a Dephosphorylation Reaction

The crystal structure of the apo form of vanadium chloroperoxidase from Curvularia inaequalis reacted with para-nitrophenylphosphate was determined at a resolution of 1.5 A. The aim of this study was to solve structural details of the dephosphorylation reaction catalyzed by this enzyme. Since the chloroperoxidase is functionally and evolutionary related to several acid phosphatases including human glucose-6-phosphatase and a group of membrane-bound lipid phosphatases, the structure sheds light on the details of the dephosphorylation catalyzed by these enzymes as well. The trapped intermediate found is bound to the active site as a metaphosphate anion PO3-, with its phosphorus atom covalently attached to the Nepsilon2 atom of His496. An apical water molecule is within hydrogen-bonding distance to the phosphorus atom of the metaphosphate, and it is in a perfect position for a nucleophilic attack on the metaphosphate-histidine intermediate to form the inorganic phosphate. This is, to our knowledge, the first structural characterization of a real reaction intermediate of the inorganic phosphate group release in a dephosphorylation reaction.

Preparation, Structure, Spectral, and Magnetic Properties of Copper(II) Halogenonicotinates: Crystal and Molecular Structure of Tetrakis(μ‐2‐chloronicotinato‐O,O′)‐diaquadicopper(II)

AbstractThe characterization of the complexes [Cu2(2‐Clnic)4(H2O)2] (1), [Cu(2,6‐Cl2nic)2(H2O)2] (2) and [Cu(5‐Brnic)2(H2O)2]n (3) (where 2‐Clnic = 2‐chloronicotinate, 2,6‐Cl2nic = 2,6‐dichloronicotinate or 5‐Brnic = 5‐bromonicotinate) was based on elemental analysis, IR, electronic and EPR spectra, and magnetic susceptibility. Complex 1 was also studied by X‐ray analysis at 298 1a and 80 K 1b. The complex 1 contains a dinuclear Cu‐acetate molecular structure in which the carboxyl groups of the 2‐chloronicotinate ligands act as bridges and water molecules are at apical positions. The stereochemistry about Cu atom at both temperatures is typical for square pyramidal geometry with CuO4O chromophore. The Cu‐Cu distance is 2.6513(8) and 2.6382(6) Å for 1a and 1b, respectively. The Cu atoms are displaced by 0.2069(9) and 0.1973(7) Å, respectively, from the plane containing four oxygen atoms bonded to the Cu atom toward the apical water molecules. Strong and weak hydrogen bonds as well as C–Cl···π interactions in the crystal structure are discussed as well. Both complexes, monomeric [Cu(2,6‐Cl2nic)2(H2O)2] (2) and polymeric [Cu(5‐Brnic)2(H2O)2]n (3), possess octahedral copper(II) stereochemistry with differing tetragonal distortions.

Anion-tuned self-assembly of zinc(II)–fluconazole complexes: Crystal structures, luminescent and thermal properties

Four novel fluconazole-bridged Zn(II) complexes, [Zn(HFlu)Cl 2(DMF)] 2 ( 1), {[Zn(HFlu) 2(H 2O) 2](NO 3) 2·2DMF} n ( 2), {[Zn(HFlu) 2(H 2O) 2](NO 3) 2} n ( 3) and {[Zn(HFlu)(SCN) 2]·H 2O} n ( 4) [HFlu = 2-(2,4-difluorophenyl)-1,3-bis(1,2,4-triazol-1-yl)-propan-2-ol], have been synthesized and structurally characterized by X-ray diffraction method. The structure of dimeric complex 1 consists of 20-membered macrometallacyclic ring-like structure, in which the Zn(II) ion is in a five-coordinated distorted trigonal bipyramidal geometry with the Zn⋯Zn distance of 10.265(3) Å across the cis HFlu ligand. Complex 2 shows infinite 1-D macrocyclic double chain structure with the central Zn(II) ions being six-coordinated by four HFlu ligands and two apical water molecules and with the intrachain Zn⋯Zn distance of 10.722(3) Å across the trans HFlu ligand. The crystal structure of complex 3 is analogous to that of complex 2 with the intrachain Zn⋯Zn distance of 10.654(2) Å. The structure of complex 4 consists of infinite 1-D coordination polymeric chain with the tetrahedral coordination geometry of Zn(II) ion and with the intrachain Zn⋯Zn distance of 11.173(2) Å across the cis HFlu ligand. Complexes 1– 4 show the similar fluorescence emission to the free HFlu ligand at ambient temperature and the thermal stabilities of the complexes have also been investigated.

Insight into the Catalytic Mechanism of Vanadium Haloperoxidases. DFT Investigation of Vanadium Cofactor Reactivity

Density functional theory (DFT) has been used to investigate the catalytic properties of the isolated vanadium cofactor found in vanadium haloperoxidases, with a particular emphasis on the steps going from the resting form of the cofactor to the peroxo complex. Computation of transition states, intermediate species, and UV-vis spectra, as well as comparison of reaction energies, demonstrated the important role of protonation in cofactor activation. This illustrates that the resting form of the vanadium cofactor reacts with hydrogen peroxide according to a mechanism that implies formation of an aqua complex, release of the apical water molecule according to a dissociative pathway, and binding of hydrogen peroxide to vanadium. This process leads to a side-on peroxo species corresponding to the peroxo form observed in the enzyme. In addition, it appears that an acid-base catalysts strongly accelerates the conversion to the side-on peroxo form. The comparison of computed and experimental UV-vis spectra corroborated the proposed reaction pathway and allowed us to explain the effects of the vanadium ligands on the electronic properties of the cofactor.

Water-dimers encapsulated in channel-containing 1D coordination polymers based on a linear dimetallic spacer

A novel one-dimensional organic–inorganic coordination polymer based on a dinuclear copper unit, formulated [Cu2(cro)4(bpp)]·H2O (Hcro=crotonic acid, bpp=1,3-bis(4-pyridyl)propane) (1) has been synthesized and characterized by X-ray crystallography, spectral, thermal, XRPD and magnetic methods. The structure of 1 is fabricated by self-assembly of integrated Cu2(cro)4·2H2O with collapse of the two apical water molecules and flexible ligand bpp into a 1D zigzag-shaped chain. Interestingly, wavy channels are formed among every four adjacent chains, and the water-dimers are situated at the apex of the channels.