Malonate Ion Research Articles

Revealing Atomic Structure of Hybrid Octacalcium-Phosphate Derivative.

Octacalcium phosphate (OCP), which is one of the bioactive calcium phosphates, can incorporate various organic molecules in its crystal lattice, forming the organic-inorganic hybrid derivatives. However, detailed atomic arrangements of OCP hybridized with organic molecules such as dicarboxylate are still unknown, although many years have passed since the first discovery of the materials systems. In the present study, some black-box optimization methods combined with first-principles calculations were used to theoretically identify the most stable atomic structure of the OCP with the incorporation of malonate ions as a typical case study. The results showed that the calculated interplanar spacing on the (100) plane of the most stable structure agrees well with experimental data, by taking account of implicit solvent of aqueous solution. An underlying mechanism that realizes the bridging feature of the incorporated malonate ions between the apatitic layers is also discussed. The present methodology can pave the way to accurately explore reliable atomic structures of such complicated organic-inorganic hybrid biomaterials with high structural degrees of freedom.

The study of the interactions of malonic acid ions with the hydroxyapatite surface in liquid

• Adsorption is described by the multiexponantiate model. • The last stage of the adsorption kinetics indicates the process of precipitation of a new phase. • Adsorption of malonic acid is best described by the Redlich-Paterson isotherm model. • The presence of adsorbed malonate ions causes an increase in the concentration of acid groups on the hydroxyapatite surface. Adsorption of malonic acid at the hydroxyapatite/aqueous NaCl solution interface based on the measurements of adsorption / desorption kinetics and adsorption as a function of pH was presented. The adsorption of malonate ions was determined from the loss of ion concentration in the solution as measured by the radioisotope using 14C labeled malonic acid. The adsorption measurements were supplemented with electrophoretic zeta potential as well as and FTIR measurements. The kinetics of adsorption from a solution with an initial concentration of 1 mmol/dm3 of malonic acid proceeds in three stages, in the last stage there was observed a rapid increase in adsorption, which proves the precipitation of a new phase by the malonate ions. The presence of this phase was confirmed by examining the crystallinity of the hydroxyapatite sample conditioned in a malonic acid solution by the method of Landi et al. on the basis of XRD patterns and measurements of particle distribution using the light scattering method.

Electrochemical Perspective on Hematite–Malonate Interactions

Organic matter (OM) interactions with minerals are essential in OM preservation against decomposition in the environment. Here, by combining potentiometric and electrophoretic measurements, we probed the mode of coordination and the role of pH-dependent electrostatic interactions between organic acids and an iron oxide surface. Specifically, we show that malonate ions adsorbed to a hematite surface in a wide pH window between 3 and 8.7 (point of zero charge). The mode of interactions varied with this pH range and depended on the acid and surface acidity constants. In the acidic environment, hematite surface potential was highly positive (+47 mV, pH 3). At pH < 4 malonate adsorption reduced the surface potential (+30 mV at pH 3) but had a negligible effect on the diffuse layer potential, consistent with the inner-sphere malonate complexation. Here, the specific and electrostatic interactions were responsible for the malonate partial dehydration and surface accumulation. These interactions weakened with an increasing pH and near PZC, the hematite surface charge was neutral on average. Adsorbed malonates started to desorb from the surface with less pronounced accumulation in the diffuse layer, which was reflected in zeta potential values. The transition between specific and non-specific sorption regimes was smooth, suggesting the coexistence of the inner- and outer-sphere complexes with a relative ratio that varied with pH.

Understanding the Steric Structures of Dicarboxylate Ions Incorporated in Octacalcium Phosphate Crystals.

Octacalcium phosphate (OCP) can incorporate various dicarboxylate ions in the interlayer spaces of its layered structure. Although not proven, these incorporated ions are believed to have a linear structure. In this study, the steric structures of twelve different dicarboxylate ions incorporated into OCP were investigated by comparing the experimentally determined interlayer distance of the OCP with the distance estimated using the molecular sizes of dicarboxylic acids calculated by considering their steric structures. The results revealed that the incorporated succinate, glutarate, adipate, pimelate, suberate, and aspartate ions possessed linear structures, whereas the incorporated azelate, sebacate, methylsuccinate, and malate ions exhibited bent structures. Further, the incorporated mercaptosuccinate ions featured linear, bent, other types of structures. Moreover, the steric structure of the incorporated malonate ion significantly differed from those of other dicarboxylate ions. The computational approach employed in this study is expected to deepen our understanding of the steric structures of dicarboxylate ions incorporated in the OCP interlayer spaces.

Synthesis and Structural Characterization of Lanthanum(III) Complexes of 4-Nitrosoantipyrine

A new series of La(III) complexes of the ligand with the general formula [La(L)2(a)3] and [La2(L)4(aa)3], (a = nitrate (1), thiocyanate (2), acetate (3) and propionate (4) ions, aa = sulphate (5), thiosulphate (6), oxalate (7) and malonate (8) ions with the ligand 4-nitrosoantipyrine (L) were synthesized and characterized using various physico-chemical studies. The primary ligand L acts as a bidentate ligand utilizing the carbonyl group and the nitroso group for bonding. The nitrate, thiocyanate, acetate and propionate ions are monovalent unidentate ligands, whereas sulphate, thiosulphate, oxalate and malonate ions are divalent bidentate ligands in the complexes 1-8. Based on spectral data and magnetic susceptibility measurements, geometry of the lanthanum(III) complexes were also proposed.

Asymmetric allylic substitution by chiral palladium catalysts: Which is more reactive, major π-allyl Pd(II) species or minor π-allyl species?

The reactivity difference of major and minor π-allyl species was examined for two typed asymmetric allylic substitutions via linear symmetrical π-allyl and linear unsymmetrical π-allyl intermediates. 31P NMR observation of the stoichiometric reaction of [Pd(1,3-diphenyl-π -allyl)(N-P-N-type ligand)]+ with malonate ion verified that major species was much more reactive than the minor one. In the case of the reaction of [Pd(1,1,3-trimethyl-π-allyl)((S)-BINAP)]+ species with soft amido ion, increase in the minor/major ratio of the π-allyl species afforded higher enantioselectivity to indicate that the minor π-allyl was more reactive than the major one.

New insights about the monomer and homodimer structures of the human AOX1.

Human aldehyde oxidase (hAOX1) is a molybdenum dependent enzyme that plays an important role in the metabolism of various compounds either endogenous or xenobiotics. Due to its promiscuity, hAOX1 plays a major role in the pharmacokinetics of many drugs and therefore has gathered a lot of attention from the scientific community and, particularly, from the pharmaceutical industry. In this work, homology modelling, molecular docking and molecular dynamics simulations were used to study the structure of the monomer and dimer of human AOX. The results with the monomer of hAOX1 allowed to shed some light on the role played by thioridazine and two malonate ions that are co-crystalized in the recent X-ray structure of hAOX1. The results show that these molecules endorse several conformational rearrangements in the binding pocket of the enzyme and these changes have an impact in the active site topology as well as in the stability of the substrate (phthalazine). The results show that the presence of both molecules open two gates located at the entrance of the binding pocket, from which results the flooding of the active site. They also endorse several modifications in the shape of the binding pocket (namely the position of Lys893) that, together with the presence of the solvent molecules, favour the release of the substrate to the solvent. Further insights were also obtained with the assembled homodimer of hAOX1. The allosteric inhibitor (THI) binds closely to the region where the dimerization of both monomers occur. These findings suggest that THI can interfere with protein dimerization.

Synthesis and X-ray Crystallographic Study of [(UO2)2(C3H2O4)(Cl)2(C4H9NO)4

Crystals of [(UO2)2(mal)(Cl)2(DMA)4] (mal2– is malonate ion and DMA is dimethylacetamide) have been synthesized and studied by X-ray crystallography. The key structure units are binuclear island complexes [(UO2)2(mal)(Cl)2(DMA)4], which belong to the A2Q02M 6 1 crystal-chemical group (A = UO 2 2+ , Q02 = mal2–, M1 = Cl– and DMA) of uranyl complexes. The complexes form a framework through a system of intermolecular nonbonded interactions, which are characterized by means of the Voronoi–Direchlet molecular polyhedron method.

Crystallographic aspects of hydrated salts of 4,6-diaminopyrimidine with the first five dicarboxylic acids

Abstract The preparation, X-ray single-crystal structure determination and vibrational spectroscopic characterisation of five novel salts, i.e. bis(4,6-diaminopyrimidinium(1+)) oxalate tetrahydrate; 4,6-diaminopyrimidinium(1+) hydrogen malonate monohydrate; bis(4,6-diaminopyrimidinium(1+)) succinate octahydrate; bis(4,6-diaminopyrimidinium(1+)) glutarate dihydrate and bis(4,6-diaminopyrimidinium (1+)) adipate octahydrate, are presented. It is the first crystallographic study with the title cation. All the structures are centrosymmetric. The oxalate, succinate and adipate anions are situated about inversion centres in their respective structures. The dependence on the parity of the number of carbon atoms in the anions is apparent in the interplanar angles of the carboxylate or carboxylic groups. In all of the structures, there are intermolecular N–H···N, N–H···Oacid, N–H···Owater, Owater–H···Oacid and Owater–H···Owater hydrogen-bonds of moderate strength. The most common graph set motif, R 2 2(8), describes the arrangement of the involved carboxylic as well as of the primary- and secondary-amine groups. There is a growing complexity of arrangement of water molecules in the structures with longer anionic molecules. In 4,6-diaminopyrimidinium(1+) hydrogen malonate monohydrate, there is an intramolecular Oacid–H···Oacid bond, and the conformation of the hydrogen malonate ions with non-parallel carboxylic and carboxylate groups is not often observed. The structural parameters of the carboxylic or carboxylate groups in the dicarboxylic acids or their derivatives found in the Cambridge Structural Database (CSD) are compared with the title structures.

Synthesis and X-ray diffraction study of uranyl malonate monohydrate

Uranyl malonate monohydrate [UO2(mal)(H2O)], where mal2– is malonate ion, was synthesized and studied by single crystal X-ray diffraction. The main structural units are electrically neutral [UO2(mal)(H2O)] layers belonging to crystal-chemical group AQ21М1 (A = UO 2 2+ , Q21 = mal2–, M1 = H2O) of uranyl complexes. Specific features of the packing of the uranium-containing complexes are discussed on the basis of Voronoi–Dirichlet tessellation. The structural differences between the monohydrate synthesized and the known uranyl malonate trihydrate are considered.

Solubilities and Glass Formation in Aqueous Solutions of the Sodium Salts of Malonic Acid With and Without Ammonium Sulfate.

The solubility of sodium hydrogen malonate and sodium malonate in water both with and without ammonium sulfate present has been studied using differential scanning calorimetry and infrared spectroscopy. The crystals that form from sodium hydrogen malonate/water solutions were determined to be sodium hydrogen malonate monohydrate by single-crystal X-ray diffractometry. The crystals formed in sodium malonate/water solutions were determined to be sodium malonate monohydrate, a compound whose structure had not been previously known. When ammonium sulfate is added to these respective aqueous systems, the precipitation solids contain sodium sulfate decahydrate under low to moderate ammonium concentrations and lecontite (NaNH4SO4·2H2O) under high ammonium concentrations, which can be found under dry atmospheric conditions. Thus, it appears the presence of malonate and hydrogen malonate ions does not significantly affect the precipitation of inorganic salts in these systems. The glass transition temperatures of all solutions were also determined, and it was observed that the addition of ammonium sulfate slightly lowers the glass transition temperature in these solutions.

The Crystal-Chemical Role of Alkylmalonate Ions in the Structure of Coordination Polymers

Alkyl-substituted (methyl, ethyl, diethyl) malonate ions (Rmal2−) are found to display 13 topologically different types of coordination with respect to d- or f-metals A. The factors that cause Rmal2− ions to choose one possible coordination are discussed; valence angle C—C—C in a malonate ion lies within 102°–119° range and depends linearly on the dihedral angle between the planes of two carboxyl groups. When coordinated with metal atom A, alkyl-substituted malonate ions are found to produce six-membered metallocycles of bath conformation. It is established that increasing the volume of R substituents in Rmal2− ions strengthens the repulsion among carboxyl groups and alkyl substituents and reduces the C—C—C angle.

Simultaneous determination of inorganic and organic ions in plant parts of Betula pendula from two different types of ecosystems (Wielkopolski National Park and Chemical Plant in Luboń, Poland).

The results of inorganic and organic anion concentrations in samples of soils and plant parts of Betula pendula (tap roots, lateral roots, stem, twigs, leaves), in the bioavailable fraction, are presented in this study. An ion chromatography method was applied for the first time in the simultaneous determination of inorganic and organic anions, as an effective tool for qualitative and quantitative analysis of samples with different matrix. A linear gradient elution with potassium hydroxide allowed for the separation of both inorganic and organic ions such as: F−, CH3COO−, HCOO−, Cl−, NO2−, Br− and NO3−, SO42−, CH2(COO)22−, C2O42−, PO43− and C3H5O(COO)33−. The samples of soils and plant parts of B. pendula from the area of the Wielkopolski National Park (WNP) and the Chemical Plant in Luboń (LU; protected vs. contaminated area) were selected for the study. The obtained results indicated that such inorganic ions as: F−, Cl−, NO3− and PO43− are quite easily transported from soil to leaves. In contrast, the mechanism of migration could not be clearly defined for SO42− because the ion was retained in roots of many of the analysed samples. Significantly higher bioavailability of inorganic ions was observed for samples collected from the area of the WNP. Phosphates were the only ions which showed no variation in their concentrations between the two sampling sites, both for soils and plant parts of B. pendula. None of the organic anions was detected in soil samples. The acetate, formate, malonate, oxalate and citrate ions were detected in all leaf samples. The statistical analysis allowed the author to determine the mechanism of ion migration and accumulation in leaves and, additionally, determine the variation in the occurrence of inorganic and organic ions depending on the sampling site (WNP vs. LU). The results of the statistical analysis were confirmed by the bioacumulation (BF) and translocation (TF) factors.

Crystal-chemical role of malonate ions in the structure of coordination polymers

In the crystal structures of the malonate-containing compounds of d- or f-metals, the C3H2O 4 2− anions were found to exhibit 17 topologically different types of coordination to the metal atoms A, playing the role of mono-, bi-, tri-, or tetradentate ligands and forming one to seven O-A bonds. The C-C-C bond angle in the malonate ions changed from 103° to 126° and depended linearly on the dihedral angle (φCOO) between the planes of the two carboxyl groups of the anion. At φCOO 67°, they can form only four-membered metallocycles. The factors that influence the conformation of malonate ions in the structures of coordination polymers were discussed.

Synthesis and crystal structure of double Ln(III) malonates with Co(NH3) 6 3+ in the outer sphere

Double Ln(III) malonates of two different compositions crystallize from malonate solutions containing [Co(NH3)6]3+ ions. Lanthanides of the beginning of the series form compounds of the composition [Co(NH3)6][Ln(mal)2]3·6H2O (I) (Ln = La, Ce, Pr, Nd; mal = C3H2O2−), and those of the end of the series form compounds of the composition [Co(NH3)6]2[Ln3(mal)7(Hmal)(H2O)4]·nH2O (II) (Ln = Tb, Ho, Er, Tm). Structure I is based on trimeric anionic complexes [Ln3(mal)6]3− linked with each other to form a branched 3D network with [Co(NH3)6]3+ cations and water molecules accommodated in large voids. The coordination mode of malonate ions in I with the coordination capacity equal to 5 was unknown previously for lanthanide malonate compounds. The Ln(1) atom has the maximum possible for malonate compounds coordination number (CN) 12, and the Ln(2) atom has CN 9. The structure of II consists of anionic chains [Ln3(mal)7(Hmal)(H2O)4]n3− between which the [Co(NH3)6]3+ cations and water molecules are arranged. One independent malonate ion in the structure is coordinated in the bidentate chelate fashion to the Ln(1) atom, and the other independent chelate-bridging ligand is coordinated in the bidentate fashion to the Ln(2) atom and in the monodentate fashion to the Ln(1) atom. As a result, tetrameric fragments linked in anionic chains are formed in the structure of II. The Ln(1) and Ln(2) atoms have CN 8.

Synthesis, Characterization and Thermal Behavior of Solid-State Compounds of Light Trivalent Lanthanide Malonates

In this study, compounds of hydrated lanthanide malonates were synthesized by precipitation of sodium malonates ion. Quantitative studies of the compounds obtained in the solid state, as well as the thermal behavior of these compounds were performed by thermal analysis (TG-DTA and DSC). Additional complementary studies were also performed using X-ray diffraction by the powder method (XRD), Evolved Gas Analysis (EGA) and complexometric titration with EDTA. Thus, the compounds synthesized in this work, ranging from lanthanum to gadolinium, were studied mainly in relation to their thermal properties, enabling to establish the stoichiometry, the decomposition steps and identify by EGA the main volatile products released during the decomposition. The qualitative study by XRD and FT-IR showed that the compounds were obtained in the crystalline state and metal-ligand coordination occurs by bidentate bonding and /or bridge, respectively. The interest in these compounds is due to the several applications of malonate ion, such as industrial and biological, not to mention that the coordination of the lanthanide ions to the malonate ligand can provide them new properties which could be studied and explored forward.

Synthesis and structure of (NH4)3[UO2(C3H2O4)2(NCS)] · 2H2O

Malonate-thiocyanate complex (NH4)3[UO2(C3H2O4)2(NCS)] · 2H2O is synthesized and studied by X-ray diffraction. The compound crystallizes in the monoclinic system: a = 13.9983(4) A, b = 8.1947(2) A, c = 16.4678(4) A, β = 100.846(1)°, space group Cc, Z = 4, and R = 0.0158. The main structural units of the crystal are mononuclear [UO2(C3H2O4)2(NCS)]3− groups belonging to the AB201M1 crystal chemical group of uranyl complexes (A = UO22+, B01 = C3H2O42−, M1 = NCS−). Discrete uranium-containing groups are connected by electrostatic interactions with ammonium ions and by hydrogen bonds. Some specific structural features of crystals containing [UO2(L)2(NCS)]3− complexes, where L is the oxalate or malonate ion, are discussed.

Stereospecific ligands and their complexes. Part XIX. Synthesis, characterization, circular dichroism and antimicrobial activity of oxalato and malonato-(S,S)-ethylenediamine-N,N′-di-2-(3-methyl)butanoato-chromate(III) complexes

The s-cis-[Cr(S,S-eddv)L]-complexes (1,2) (S,S-eddv=(S,S)-ethylenediamine-N,N′-di-2-(3-methyl)butanoato ion; L=oxalate or malonate ion) were prepared. The complexes were purified by ion-exchange chromatography. The geometry of the complexes has been supposed on the basis of the infrared and electronic absorption spectra, and the absolute configurations of the isolated s-cis-[Cr(S,S-eddv)L]-complexes have been predicted on the basis of their circular dichroism (CD) spectra. Also, the results of thermal decomposition have been discussed. Antimicrobial activity of the prepared complexes (1–4) was investigated against 28 species of microorganisms. Testing was performed by microdilution method and minimum inhibitory concentrations (MIC) and minimum microbicidal concentration (MMC) have been determined. Complexes demonstrated in generally low antibacterial and antifungal activity.

Supramolecular structures of metal complexes containing barbiturate and 1,2-bis(4-pyridyl)-ethane

This work describes the synthesis, thermal, spectroscopic properties (Raman and infrared), and crystal structures of five new supramolecular compounds [Mn(bpa)(H2O)4]B2 · 4H2O (1), [Fe(bpa)(H2O)4]B2 · 4H2O (2), [Co(bpa)(H2O)4]B2 · 4H2O (3), [Zn(bpa)(H2O)4]B2 · 4H2O (4), and Co2mal2bpa · 2H2O (5), where B is the anion of barbituric acid, bpa is 1,2-bis(4-pyridyl)-ethane, and mal is malonate ion. Compounds 1–4 are isostructural, showing covalent linear 1-D [M(bpa)(H2O)4]2+ chains, which interact by hydrogen-bonding and π-stacking interactions with barbiturate and crystallization water molecules resulting in a 3-D arrangement, belonging to Pbcn space group. Compound 5 has been obtained from the opening of the barbituric acid ring, with the formation of malonate, coordinated simultaneously to three cobalts in a 1-D chain along the c-axis, whereas bpa ligand gives rise to another 1-D chain along the a- and b-axes, resulting in a 3-D coordination polymer containing cavities. The vibrational spectra of 1–4 are also very similar; Raman spectra display two intense bands related to bpa at 1616 and 1020 cm−1, assigned to the (ν CC/ν CN) and ring stretching modes, respectively. The barbiturate is also confirmed by a band at 684 cm−1; the interesting point to be emphasized is this vibrational mode is not observed for 5, corroborating the absence of this building block in the structure.

2-Amino-5-chloro-pyridinium 2-carb-oxy-acetate.

The title salt, C5H6ClN2 +·C3H3O4 −, contains two cations and two anions in the asymmetric unit. Both 2-amino-5-chloro­pyridinium ions are protonated at their pyridine N atoms and both hydrogen malonate ions feature an intra­molecular O—H⋯O hydrogen bond, which generates an S(6) ring motif and results in a folded conformation. In the crystal structure, the cations and anions are linked via N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds, forming chains propagating in [010], which are cross-linked by further C—H⋯O inter­actions.