Crystal Structures Of Sodium Research Articles

Negative Linear Compressibility of Formate Crystals from the Viewpoint of Quantum Electronic Pressure

In order to understand the phenomenon of negative linear compressibility (NLC) in organic crystals, it is necessary to investigate not only the structural features but also the electronic changes taking place under external hydrostatic pressure. It is also necessary to clarify which electronic properties allow the quantification and comparison of the compressibility of crystals. In our study, the crystal structures of sodium and cadmium formates under hydrostatic compression were modeled, as well as the α and β-phases of calcium formate. The changes in cell parameters and spatial dependences of the linear compressibility were analyzed, and the ranges of external pressure, which must be applied for NLC onset, were predicted for the sodium and α-calcium formates. Although the behavior of chemical bonds is not predicted by the sign or absolute value of the quantum electronic pressure, its relative change under external pressure clearly distinguishes the soft and rigid regions in a crystal. The relationship between the NLC values and the changes in quantum electronic pressure in the cavities of formate crystals was established.

Crystallographic new light on an old complex: NaMg[Cr(oxalato)3]·9H2O and structure redetermination of the isomorphous aluminum(III) compound

The crystal structure of sodium and magnesium tris(oxalato)chromato(III) nona hydrate, NaMg[Cr(C2O4)3]·9H2O, has been determined by X-ray diffraction methods. It crystallizes in the trigonal P3c1 space group with (in the hexagonal setting) a = b = 16.9635(4), c = 12.5247(3) Å, and Z = 6 molecules per unit cell. The Cr(III) and sodium ions are in octahedral environments coordinated to three oxalate molecules and arranged in a honeycomb-like layered structure perpendicular to the crystal c-axis. There are three different octahedral [Mg(H2O)6]2+ hydrated ions that fill the honeycomb holes giving rise to electrically neutral Na[Mg(H2O)6][Cr(oxalato)3] crystal slabs. Neighboring slabs are bridged by the remaining three water molecules through H-bonds and therefore the whole crystal can be more properly described as Na[Mg(H2O)6][Cr(oxalato)3]·3H2O. Also, the structure of isomorphous NaMg[Al(C2O4)3]·9H2O compound has been re-examined and compared with the chromium(III) complex. Infrared and Raman spectra of both complexes were also recorded and briefly discussed.

One-dimensional coordination polymers in the crystal structures of sodium and potassium acetylacetonates

The mixed ligand complexes [K2(acac)2(H2O)]∞ (I), [K2(acac)2(phen)(H2O)]∞ (II), [Na(acac)(H2O)]∞ (III), [Na3(acac)3(iPrOH)]∞ (IV), [Na3(acac)3(Py)]∞ (V) and [Na2(acac)2(phen)]∞ (VI) (Hacac=pentane-2,4-dione; phen=1,10-phenanthroline; iPrOH=iso-propanol; Py=pyridine) were synthesized by the reaction of the alkaline metal tert-butyloxide in dried solvent (iPrOH, benzene or Py) with Hacac and phen. The products were characterized by elemental analysis, 1H NMR and FTIR spectroscopy, and thermal analysis. The single-crystal structures were determined for the novel compounds II, IV and VI, and refined for I. The structures of I–VI consist of one-dimensional polymeric chains or ribbons which are described as a combination of formal binuclear structural blocks, [M2(acac)2], of four types. Quantum chemical calculations on the four isomers of [M2(acac)2] allowed us to explain different stabilities of the formal building blocks with M=Na and K.

Hydrothermal Synthesis and Crystal Structure of Sodium(2S)-2-amino-5-hydroxy-5-oxo-pentanoate

Hydrothermal Synthesis and Crystal Structure of Sodium(2S)-2-amino-5-hydroxy-5-oxo-pentanoate

Synthesis, Characterization, and Crystal Structure of Sodium (Methyl α-d-Mannopyranosid)uronate Monohydrate

TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl)-mediated oxidation of methyl α-<sc>d</sc>-mannopyranoside with sodium hypochlorite gave sodium (methyl α-<sc>d</sc>-mannopyranosid)uronate, which was obtained as a crystalline monohydrate in ~70% yield without chromatography. Its purity was proved by NMR spectroscopy, a newly developed HPLC method, combustion analysis, and X-ray crystallography. The crystal structure, solved from synchrotron diffraction data in space group <i>P</i>2₁2₁2₁, revealed that the packing of the uronate molecules is connected by an extensive network of hydrogen bonds, and that the Na⁺ ion is coordinated by six oxygen ligands from one water and three surrounding sugar molecules.

Synthesis and Crystal Structures of Sodium and Calcium ­Complexes with the Ligand N‐(2,6‐Dimethylphenyl)diphenylphosphinic Amide

AbstractThe sodium complex [{Ph2P(O)NH(2,6‐Me2C6H3)}Na{Ph2P(O)N(2,6‐Me2C6H3)}]2 (2) with the ligand N‐(2,6‐dimethylphenyl)diphenylphosphinic amide was synthesized involving the reaction of the neutral ligand [Ph2P(O)NH(2,6‐Me2C6H3)] (1) and sodium bis(trimethylsilyl)amide in toluene at 60 °C. The calcium complex [{Ph2P(O)NH(2,6‐Me2C6H3)CaI(THF)3}I] (3) was obtained by the reaction between the neutral ligand 1 and anhydrous calcium diiodide in THF at ambient temperature. The solid‐state structures of the complexes were established by single‐crystal X‐ray diffraction analysis. In the solid‐state structure of 2, the sodium ion is coordinated through the chelation of oxygen atom attached to the phosphorus atom. Two different P–N and P–O bond lengths are observed, which indicates that one ligand moiety is anionic, whereas the second one is neutral. In the solid‐state structure of 3, the calcium atom adopts distorted octahedral arrangement through the ligation of two phosphinic amide ligands, three THF molecules, and one iodide ion.

Arginine Movement in Synergistic Coupling of Substrate and Ion Binding to Glutamate Transporter Homologue

Glutamate transporters are membrane pumps, which catalyze reuptake of the neurotransmitter from the brain synapses driven primarily by symport of sodium ions. A bacterial homologue, GltPh is a sodium/aspartate symporter, for which the crystal structures of sodium and substrate bound states have been determined. The thermodynamic studies have demonstrated that binding of sodium ions and aspartate to the transporter are coupled, such that the affinity for the substrate is much higher in the presence of the ions and vice versa. However, the ions are not directly coordinated by the substrate and the molecular mechanism of coupling remains largely unknown. Arginine 397 interacts with the side chain carboxylate of the substrate in the transporter crystal structures, is highly conserved among glutamate transporters, and has been shown in functional studies to be a key residue for substrate binding in mammalian homologues. To probe how the formation of the substrate-binding site affects sodium binding, we generated R397A mutant. We show that, as expected, R397A mutant has a low substrate affinity even in the presence of 100 mM sodium, measured by the isothermal titration calorimetry. Remarkably, in the absence of aspartate the sodium binding affinity for R397A is increased by ∼10 fold, compared to the wild type transporter, as measured by a fluorescence assay in vitro. Furthermore, substrate does not significantly increase the affinity of the mutant transporter for the ions. We suggest that arginine 397 in the wild type GltPh interferes with the sodium binding site or sites in the absence of the substrate and that its re-orientation upon substrate coordination relieves this interference. We hypothesize that these events are key to the mechanism of the allosteric coupling between substrate and ion binding.

Synthesis and Structures of 3,5-disubstituted 1,2,4-triazole Head Units and Incorporation of 3,5-dibenzoyl-1,2,4-triazolate into New [2 + 2] Schiff-Base Macrocyclic Complexes

The synthesis and characterization of sodium 3,5-diacetyl-1,2,4-triazolate (4 Me ) and sodium 3,5-dibenzoyl-1,2,4-triazolate (4 Ph ), both of which can be used as head unit building blocks in Schiff-base reactions, are reported. The crystal structures of sodium 3,5-diacetyl-1,2,4-triazolate, as [4 Me (H2O)]∞, and sodium 3,5-dibenzoyl-1,2,4-triazolate, as [4 Ph (CH3OH)2]2, have been determined. The former is a helical polymer whilst the latter is a methanol-bridged dimer. The lead(II) templated cyclization reaction of sodium 3,5-dibenzoyl-1,2,4-triazolate (4 Ph ) with 1,3-diaminopropane or 1,4-diaminobutane, respectively, leads to the formation of two new [2 + 2] Schiff-base macrocycles as their lead(II) complexes, [Pb2 L 3Ph (μ-OH)]ClO4 (5) and [Pb2 L 4Ph (μ-OH)]ClO4 (6), respectively. Transmetallation of 5 with nickel(II) ions yields a novel, structurally characterized, dinickel(II) macrocyclic complex, [Ni2 L 3Ph (NCS)2] (7), which features double triazolate bridging of the two five-coordinate nickel(II) ions.

The coordination properties of aminobenzoate ligands in complexes with alkali metals

The crystal structures of sodium 4-amino-2-hydroxybenzoate dihydrate [NaL·2H2O, L = C6H3(NH2)(OH)COO] and potassium 2-aminobenzoate monohydrate [KL*·H2O, L* = C6H4(NH2)COO] were determined by X-ray diffraction methods. The compound NaL·2H2O crystallizes in the monoclinic system, space group P21/c with a = 8.820(2), b = 14.632(3), c = 6.948(2) Å, β = 97.88(3)°. The structure consists of sodium ion pairs joined together by tridentate 4-amino-2-hydroxybenzoate moieties creating a polymeric chain. In the metal centres, two water molecules bridge the sodium atoms. Five oxygen atoms and one nitrogen atom form a distorted octahedral environment. The compound KL*·H2O crystallizes in the monoclinic system, space group P21/c with a = 14.684(3), b = 7.618(2), c = 7.512(2) Å, β = 96.95(3)°. The structure consists of octacoordinated potassium atoms bonded with three water molecules and five carboxylate oxygen atoms. Water molecules appear as bridging ligands. The 2-aminobenzoate ligand acts as a pentadentate ligand with the molecular network stabilized by hydrogen bonds. Among the polymeric chains in both structures appear noncovalent interactions of type N−H···X.

Physicochemical properties of solutions of bis(2,3,5,6-tetraoxo-4-nitropyridinate) dianions. Crystal structures of sodium 2,3,5,6-tetraoxo-4-nitropyridinate trihydrate and sodium ammonium bis(2,3,5,6-tetraoxo-4-nitropyridinate) monohydrate

Ammonium 2,3,5,6-tetraoxo-4-nitropyridinate was shown to exist as stable dimers and act as a weak electrolyte in both a crystalline state and aqueous solutions. In a strongly alkaline medium, ammonium cations were successively replaced by sodium cations. The molecular and crystal structures of sodium 2,3,5,6-tetraoxo-4-nitropyridinate trihydrate and sodium ammonium bis(2,3,5,6-tetraoxo-4-nitropyridinate) monohydrate were established, and their spectroscopic characteristics were determined.

Synthesis and crystal structure of sodium and caesium ion complexes of unsubstituted calix[4]arene.: New polymeric chain arrangements

Calix[4]arene, devoid of p-alkyl substituents, has been used to complex sodium and caesium ions in a basic medium. The crystal structures of one sodium and two caesium complexes are reported and compared to previous structures with related p- tert-butylcalixarenes. The sodium complex is dimeric, two cations being sandwiched between two mono-anionic calixarenes through O-coordination, and bound also to three acetone molecules (one bridging) in the median plane. Both caesium complexes are polymeric, with a stacking of alternate cations and mono-anionic calixarenes, with both polyhapto bonding and O-coordination. This novel arrangement is attributed to the lack of bulky p-substituents in the ligand, which enables the cation included in the cavity of one calixarene to be closely approached by the oxygen donors of a second one on the other side.

Rerefinement of sodium thiosulfate pentahydrate

The crystal structure of sodium thio­sulfate penta­hydrate, Na2S2O3.5H2O, has been refined to an R value of 0.022 for 1621 observed reflections. All the water-H atoms were located.

Polynuclear coordination compounds of alkali metal ions with organic chromophores.

The crystal structures of sodium 4-([4-[N,N-bis(2-hydroxyethyl)amino]phenyl]diazenyl)benzoate 3.5-hydrate, Na+*C17H18N3O4-*3.5H2O, (I), and potassium 4-([4-[N,N-bis(2-hydroxyethyl)amino]phenyl]diazenyl)benzoate dihydrate, K+*C17H18N3O4-*2H2O, (II), are described. The results indicate an octahedral coordination around sodium in (I) and a trigonal prismatic coordination around potassium in (II). In both cases, coordination around the metal cation is achieved through O atoms of the water molecules and hydroxy groups of the chromophore. The organic conjugated part of the chromophore is approximately planar in (I), while a dihedral angle of 30.7 (2) degrees between the planes of the phenyl rings is observed in (II).

Intercalation of cations in crystalline anionic surfactants

Crystal structures of sodium, potassium and cesium salts of anionic surfactants, methyl 2-sulfoalkanoates, were analyzed by X-ray methods to characterize physico-chemical properties of the solid state in relation to counter ions. The crystal contains racemic molecules with the stereogenic β carbon atom. The crystals have a bilayer structure with the interdigitated alkyl chain of anions, while the cations and water molecules are intercalated between the layers. These crystals have different thermal stability indicated by the decrease in melting temperature in the order of potassium, cesium and sodium salts. The crystals of sodium, potassium and cesium salts contain two, one and one water molecules, respectively. The space group is Pbca for all of these crystals having the same type of crystal packing of anions regardless of the different cations. The crystal packing of the potassium salts is not significantly affected by the alkyl chain length, except for the difference in the c dimension. The energetic difference of the crystal structures was analyzed by molecular mechanics calculations using X-ray coordinates. The thermal stability of the crystal is related to the crystal structure, especially to the packing of cations and sulfonato groups between the layers. The potassium ion contributes more to the thermal stabilization of the crystal than the sodium and cesium ions because of more effective contact with the sulfonato groups by less coordination with the water molecule and by acquired electrostatic potential. The close packing of ionic layers observed in the crystals of potassium salts causes dense packing of the alkyl chains which stabilizes the crystal packing.

Binding properties of carbohydrate sulfamates based on ab initio [formula omitted] calculations on N-methyl and N-ethyl sulfamate anions

2-Deoxy-2-sulfoamino- d-glucopyranoside anions are uniquely found in heparin-like biopolymers. Due to the bioactivities of these biopolymers, there is considerable interest in developing heparin mimetics as potential therapeutic agents. The chemical bonding of such anions is analyzed by topological analysis of the electron-density distribution based on ab initio 6–31 + G ∗∗ calculations. The results support an amine-like pyramidal geometry for nitrogen with a well-defined maximum in the Laplacian of the charge density consistent with a lone pair of electrons. Water complexes of the N-methyl sulfamate anions give insight into binding motifs, including bifurcated hydrogen-bonded systems and hydrogen-bond properties for the sulfoamino nitrogen. Finally, by systematic variation of the structural parameters of these N-alkyl sulfamate anions, MM + parameters for this group in sugars were determined. The structural properties calculated by molecular modeling agree well with the ab initio results and with three crystal structures of sodium 2-deoxy-2-sulfoamino-α- d-glucopyranose derivatives.

A hydrate of the sodium salt of a penem carboxylic acid

The crystal structure of sodium (5R,6S)-6-[(R)-1-hydroxyethyl]-7-oxo-3-[(R)-2-tetrahydrofuryl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylate 2.5-hydrate, Na + .C 12 H 14 NO 5 S - .5/2H 2 O, a member of a new class of β-lactam antibiotics, has been determined by X-ray diffraction. The C(3)-S(1) bond (bridgehead C atom) is longer than the C(2)-S(1) bond, although the latter is usually longer in penicillins and cephalosporins. The crystal packing shows a three-layer sheet in which two layers of the molecules are held together by Na + ions and by water molecules through a network of hydrogen bonds

X-Ray Crystal Structure Determination of Some Sodium Anthraquinone Sulfonate Derivatives

The crystal structures of sodium 9,10-dioxo-9,10-dihydroanthracene-2-sulfonate hydrate (1) and sodium 9,10-dioxo-9,10-dihydroanthracene-1,5-disulfonate trihydrate (2) have been determined by single-crystal X-ray diffraction at 253 K and refined to R 0.03 for (1) (1535 reflections) and R 0.04 for (2) (1409 reflections). Crystals of (1) are monoclinic, P21, a 17.395(5), b 6.625(2), c 5.537(1)Ǻ, β 91.87(2)°, Z 2, and those of (2) are orthorhombic, Pnma, a 11.332(4), b 20.048(5), c 7.634(3)Ǻ, Z 4. The results of molecular mechanics calculations on these two molecules were in general agreement with those determined by X-ray methods. The effect of sulfonate substitution in the 1-position compared with that in the 2-position include a small lengthening of the C-S bond and a displacement of the sulfur and quinone oxygen atoms to opposite sides of the plane of the substituted aromatic ring. However, these differences do not appear to be of sufficient magnitude to account for the much greater differences in the electrochemical and photochemical behaviour of these two classes of anthraquinone sulfonate derivatives.

The preparation and crystal structures of sodium and potassium pentamethylcyclopentadienyl pyridine solvates

The compounds (C 5Me 5)Na · 2py ( 2) have been prepared and their crystal structures determined at low temperatures. The crystal structure of 1 exhibits a three-legged stool monomer of composition (C 5Me 5Na · 3py, whereas 2 has a linear zig-zag chain structure of composition [(C 5Me 5)K · 2py] oo.

The cyclic structure of 2-iodosyl- and 2-iodyl-benzoic acid anions: a basicity and X-ray crystallographic study

The crystal structures of sodium 2-iodosyl-4-nitrobenzoate and sodium 2-iodyl-4-nitrobenzoate demonstrate a bicyclic structure for each, pKa, considerations indicate that the anions remain cyclized in solution. The crystal structure of 2-iodyl-5-methylbenzoic acid has also been obtained.

From crystal to micelle: A new approach to the micellar structure

The structure of sodium and rubidium deoxycholate micellar aggregates in aqueous solutions was found to be helical and to be stabilized mainly by polar interactions. Astonishingly, the lateral surface of the helix is covered by nonpolar groups and the interior part is filled with cations surrounded by water molecules, as in the case of an inverted micelle. This helical model was inferred from the crystal structures of sodium and rubidium deoxycholates and proved by spectroscopic and diffractometric experimental data. The strategy of the approach to the determination of the micellar structure and the comparison with another model, previously proposed for the bile salt micelles, are reported. On the basis of some results obtained for sodium tauro- and glyco-deoxycholates, micellar models are suggested which could account for the biological function of these important conjugated bile salts.