Crystal structures of monohalogenated benzoic acids

Crystal structures resulting from a combination of different types of specific intermolecular interactions have been analysed using examples of 12 monohalogenated benzoic acids (HBA). These have been compared with structures known for corresponding monofunctional compounds, namely benzoic acid, fluorobenzene, chlorobenzene and iodobenzene. It is found that common for carboxylic acids centrosymmetric hydrogen-bonded dimers exist in all HBA, and at the same time a degree of halogen atoms aggregation is rather high in the most part of HBA, similarly to chlorobenzene and iodobenzene crystals. Previously reported tendency to increasing degree of Hal-aggregation in the sequence F < Cl ≤ Br ≤ I is confirmed. It is remarkable that a stacking motif of benzene rings is realised in all HBA crystals though it is absent in all considered monofunctional substances.     

Copper-catalyzed amidation of benzoic acids using tetraalkylthiuram disulfides as amine sources

A facile method for the copper-catalyzed synthesis of N-substituted benzamides was explored. In the presence of CuBr and di-tert-butyl peroxide, various N-substituted benzamides were prepared through amidation of benzoic acid by using commercially available and cheap tetraalkylthiuram disulfides as amine sources. With this protocol, a series of 14 N-substituted benzamides were furnished in good to excellent yields. The broad substrate scope and good to excellent yield show its practical synthetic value in organic synthesis.     

Application of linear-sweep voltammetry to the determination of nucleic acids using crystal violet as an electrochemical probe

A new linear-sweep voltammetric assay of nucleic acids (NAs) based on their interaction with crystal violet (CV) is proposed. In a pH 3.5 Britton—Robinson (B-R) buffer solution, CV had an irreversible voltammetric reductive peak at −0.77 V and the peak current greatly decreased by the addition of NAs. Under the experimental conditions, the decrease in the peak current was used for the NAs assay 0.5–18.0 μg/mL of fish sperm DNA, 0.6–15.0 μg/mL of calf thymus DNA, and 0.8–12.0 μg/mL of yeast RNA. The detection limits (3σ) were 0.32, 0.47, and 0.61 μg/mL for fsDNA, ctDNA, and yRNA, respectively. The binding reaction can be completed after mixing DNA with CV within 10 min and the electrochemical response is stable for 2 h. There are seldom interferences in this method and three synthetic samples were analyzed with satisfactory results. The stoichiometry of the supramolecular complex with the binding number 3 and the binding constant 2.78 × 10¹⁴ is calculated using electrochemical data. The text was submitted by the authors in English.     

Ionization of five aqueous fluorobenzoic acids: Conductance and thermodynamics

The three monofluorobenzoic acids together with 2,4-difluoro and 2,6-difluorobenzoic acids in aqueous solution are the subject of precision conductance measurements. The experimental data are analyzed to give ionization constants and limiting conductances at temperatures from 0 to 100°C. Walden products for the acid anions are derived from the limiting conductances while the ionization consatants are fitted by statistical methods to the function pK _a (m)=A+B/T+ C logT+DT. Only the 2,6- acid requires the fourth term of the function to fit the data to a precision of better than 0.03%. Mathematical analysis of the pK function gives the standard changes in enthalpy, entropy, and heat capacity. All the acids studied are more acidic than the parent, benzoic acid, as well as more acidic than the isoelectronic methylbenzoic acids. In general the increased acidity is tied to decreases in enthalpy while entropy changes on ionization differn little from those found for the parent acid.     

Synthesis and crystal structure of a meloxicam co-crystal with benzoic acid

Structural Chemistry - Single crystals of a 1:1 co-crystal of meloxicam [4-hydroxy-2-methyl-N-(5-methyl-1,3-thiazol-2-yl)-1,1-dioxo-2H-1λ6,2-benzothiazine-3-carboxamide], MXM, with benzoic...     

Detection-dependent kinetics as a probe of folding landscape microstructure

The folding landscapes of polypeptides and proteins exhibit a hierarchy of local minima. The causes range from proline isomerization all the way down to microstructure in the free energy caused by residual frustration inherent in even the best 20 amino acid design. The corresponding time scales range from hours to submicroseconds. The smallest microstructures are difficult to detect. We have measured the folding/unfolding kinetics of the engineered trpzip2 peptide at different tryptophan fluorescence wavelengths, each yielding a different rate. Wavelength-dependent folding kinetics on 0.1-2 mus time scales show that different microstructures with a range of solvent exposure and local dynamics are populated. We estimate a lower limit for the roughness of the free energy surface based on the range of rates observed.     

Determination of nucleic acids using calcein-neodymium complex as a fluorescence probe.

A novel fluorometric method has been developed for rapid determination of DNA and RNA with calcein-neodymium complex as a fluorescence probe. The method is based on the fluorescence enhancement of calcein-Nd(III) complex in the presence of DNA or RNA, with maximum excitation and emission wavelength at 489 nm and 514 nm, respectively. Under optimal conditions, the calibration graphs are linear over the range 0.5 - 3.0 microg/ml for both DNA and yeast RNA, 0.4 - 2.0 microg/ml for fish sperm DNA (FS DNA) and 0 - 3.0 microg/ml for calf thymus DNA (CT DNA). The corresponding detection limits are 15.1 ng/ml for DNA, 21.2 ng/ml for yeast RNA, 10.5 ng/ml for FS DNA and 8.9 ng/ml for CT DNA. The interaction mechanism for the binding of calcein-Nd(III) complex to DNA is also studied. The results of absorption spectra, fluorescence polarization measurements and thermal denaturation experiments, suggested that the interaction between calcein-Nd(III) complex and DNA is an electrostatic interaction.     

Molecular structures of triethylamine complexes with benzoic and pivalic acids

Dissolution of benzoic or pivalic acid in excess triethylamine followed by crystallization was found to yield single crystals of 1: 1 and 1: 2 complexes, respectively. X-ray crystallography have shown that the complex with benzoic acid is an (Et₃NH)⁺(OOCPh)^? ion pair, in which the proton is transfered from the acid to the base (N?O 2.629(2) Å), and the complex with pivalic acid contains, in addition to the ion pair (N?O 2.649 Å), the homoconjugate anion (Bu^tCOO)(H)(OOCBu^t)^? (O?O 2.521 Å).     

Synthesis,structures and properties of ternary rare earth complexes with fluorobenzoic acid and 1,10-phenanthroline

Three dimeric rare-earth complexes [Eu(p-FBA)₃(phen)(H₂O)]₂ (1), [Tb(p-FBA)₃phen]₂ (2), and [Tb(o-FBA)₃phen]₂ (3) (where p-FBA = p-fluorobenzoate, o-FBA = o-fluorobenzoate, phen = 1,10-phenanthroline) were synthesized and structurally characterized. All are neutral dimeric molecules. Complex 1 crystallizes in triclinic system, space group P 1. Each Eu(III) ion is eight-coordinate with one 1,10-phenanthroline, one monodentate carboxylate, one water and four bridging carboxylates. Complex 2 crystallizes in triclinic system, space group P 1. Each Tb(III) is also eight-coordinate with one 1,10-phenanthroline molecule, one bidentate chelating carboxylate and four bridging carboxylates. Complex 3 crystallizes in the monoclinic system, space group P2₁/c and consists of two crystallographically different binuclear molecules. Tb(III) ions are eight-coordinate with one 1,10-phenanthroline, one bidentate chelating carboxylate and four bridging carboxylates in both of them. Complex 1 shows bright red luminescence, 2 and 3 show green luminescence under UV light at room temperature. Thermal analysis indicates that are all quite stable to heat.     

Structural change from homogenous structure to staging in benzoic acid intercalated LDH: experimental and molecular dynamics simulation insights

The intercalation the of 4,4'-oxybis(benzoic acid) anion (OBA(2-)) into MgAl-layered double hydroxide (LDH) was carried out in formamide, and the structural change of the nanocomposites from homogenous to staging was investigated through in situ XRD, FT-IR, TG-DSC, SEM and molecular dynamics (MD) simulations. In both formamide and water, the nanocomposites had a homogenous structure with a basal spacing of ～1.7 nm, showing the configuration of OBA(2-) was vertical to the LDH layers; however, with a decrease in water content after drying, the structure changed to a staging with a basal spacing of 2.62 nm. This resulted from the 1.72 nm phase and another one of 0.85 nm, which was produced by the configuration of OBA(2-) horizontal to the LDH layers. MD simulations revealed that the LDH layers distorted surrounding OBA(2-), and the deformation became more severe with decreasing water content in the interlayer, leading to the staging formation. The simulated XRD pattern confirmed that the staging observed in the experimental pattern was of the Daumas-Hérold type.     

Sulfonyl-bridged oligo(benzoic acid)s: synthesis, X-ray structures, and properties as metal extractants

Sulfonyl-bridged oligo(benzoic acid)s 7 _n (n = 2–4) are prepared from the corresponding triflate esters (8 _n ) of sulfur-bridged oligophenols by palladium-catalyzed methoxycarbonylation of the triflate moieties, followed by hydrolysis of the resulting methyl esters, and subsequent oxidation of the sulfur bridges. X-ray analysis reveals that dimer 7 ₂ forms supramolecular zig-zag chains through intermolecular hydrogen bonds between the carboxy groups. As for the crystal of trimer 7 ₃ , two molecules are associated through two couples of intermolecular hydrogen bonds between terminal and central carboxy groups to form a cyclic dimer, which connects with two adjacent dimers with the remaining carboxy groups to construct an infinite columnar structure. Tetramer 7 ₄ adopts a monomolecular cyclic structure through intramolecular hydrogen bonds between the terminal carboxy groups, and a molecule connects with each of two adjacent molecules through two couples of intermolecular hydrogen bonds between inner carboxy and sulfonyl groups. Solvent extraction experiments reveal that the oligo(benzoic acid)s exhibit high extractability toward lanthanoid ions (Ln³⁺); the performance follows the order 7 ₄  ≈ 7 ₃  > 7 ₂ . Moderate extraction selectivity is observed for the extraction of Pr³⁺, Gd³⁺, and Yb³⁺ with 7 ₂ . X-ray crystallographic analysis of cluster [Tb₄L₄(H₂O)₆](Et₃NH)₄, which was prepared from 7 ₄ (H₄L) and Tb(NO₃)₃·6H₂O in the presence of Et₃N, reveals that no sulfonyl oxygens coordinate to the metal centers. This indicates that the high extractability of 7 ₄ originates from the electron-withdrawing nature of the sulfonyl function, which increases the acidity of two adjacent carboxy groups.     

Regio-selective hydroxysubstitution of fluorobenzoic acid derivatives: facile synthesis of fluorosalicylic acid derivatives

Ortho-substituted fluorine in 2,4-difluorobenzoic acid was found to be regio-selectively replaced to hydroxide by solid sodium hydroxide in 1,3-dimethyl-2-imidazolidinone, to afford 4-fluoro-2-hydroxybenzoic acid in high yield. Several multi-fluoro-substituted benzoic acid derivatives were effectively transformed to the corresponding salicylic acid derivatives under the similar conditions.     

Capillary zone electrophoretic separation of isomeric benzoic acids using cyclodextrin

A method using capillary zone electrophoresis has been developed for separation of a series of isomeric benzene polycarboxylic acids. The separation was found to depend largely on the geometry of the acids and their degree of ionization as well as on the buffer pH and composition. The presence of additives to the buffer such as cyclodextrin and cationic surfactants was found necessary for complete resolution of all the isomers.     

A novel fluorescent method for determination of peroxynitrite using folic acid as a probe

A novel method for the determination of peroxynitrite using folic acid as a fluorescent probe is described. The method is based on the oxidation of the reduced, low-fluorescent folic acid by peroxynitrite to produce a high-fluorescent emission product. The fluorescence increase is linearly related to the concentration of peroxynitrite in the range of 3 × 10⁻⁸ to 5.0 × 10⁻⁶ mol L⁻¹ with a correlation coefficient of 0.998, and the detection limit is 1 × 10⁻⁸ mol L⁻¹. Interferences from some metal ions normally seen in biological samples, and also some anions structurally similar to peroxynitrite were studied. The optimal conditions for the detection of peroxynitrite were evaluated.     

Fluorescence enhancement method for the determination of nucleic acids using cationic cyanine as a fluorescence probe

A fluorescence enhancement method with a cationic cyanine as a probe was developed for the determination of nucleic acids. Under the experimental conditions, the fluorescence enhancement of cyanine (lambda(ex)/lambda(em)= 524/591.5 nm) was observed in the presence of DNA. The calibration graphs were linear over the range of 0.01-15 microg mL(-1) for both calf thymus DNA (CT DNA) and fish sperm DNA (FS DNA). The limits of detection were 0.005 and 0.007 microg mL(-1) for CT DNA and FS DNA, respectively. The method was applied to the determination of DNA in synthetic and real samples and satisfactory results were obtained. A possible fluorescence enhancement mechanism was also studied.     

3,4-二羟基苯甲酸镉配合物的合成,结构表征及荧光性质

采用碳酸镉和3,4-二羟基苯甲酸、2,2’-联吡啶合反应得到了配位聚合物[Cd(C7H5O4)2·(H2O)3·2H2O(1).采用元素分析、红外光谱、荧光光谱对配合物进行了表征.用X射线单晶衍射仪测定了配合物的晶体结构.配合物为单斜晶系,P2(1)/c空间群,昌胞参数Z=4,a=0.78338(8)nm,b=1.98...     

Structural studies of C-amidated amino acids and peptides: crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2

As part of the series investigating the structural features of C-terminal amidated amino acids and peptides, three crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2 were analyzed by the X-ray diffraction method, and their molecular conformations and intermolecular interactions were investigated. Although the respective dipeptides exhibited an energetically allowable torsion angle concerning each backbone or side chain, the observed extended (Z-Gly-Phe-NH2, Asp-Phe-NH2) and folded (Tyr-Lys-NH2) conformations were considerably different from those of the corresponding unamidated peptides, due to the conformational flexibility of the respective dipeptides. The comparison between the crystal packings of the amidated and unamidated dipeptides indicated that the C-terminal amides tend to associate with the same neighboring group through hydrogen bonds, in which both the amide NH and O=C groups participate, while the unamidated peptides prefer a linear molecular connection, where both or either of the two carboxyl oxygens participate in the hydrogen bond formation. The difference in hydrogen bonding ability between the C-terminal amide and carboxyl groups has been considered to be based on the structural data of the related peptides analyzed so far.     

Generation of benzyne from benzoic acid using C-H activation

ortho C-H activation of benzoic acids with Pd(II) generates an oxapalladacycle that can decarboxylate to produce a palladium-associated aryne. The arynes then undergo [2+2+2] trimerisation to afford triphenylenes.     

New mesogens with cubic phases: hydrogen-bonded bipyridines and siloxane-containing benzoic acids II. Structural studies

The supramolecular structure of new hydrogen-bonded mesogens composed of dipyridyl and 4-(oligodimethylsiloxyl)alkoxybenzoic acids was investigated by X-ray diffraction and deuterium NMR. These H-bonded mesogens exhibit a cubic thermotropic liquid crystalline phase at a temperature below a smectic A phase. Moreover, above the smectic A phase two optically isotropic, low viscosity phases (I₁ and I₂) exist with the lower temperature I₁ phase comprising aggregated mesogens. Two broad, temperature-independent, wide angle X-ray reflections suggest that the aggregation is driven by nanophase-separation; the aggregate adopts a structure with one domain siloxane rich and the other hydrocarbon rich. In the isotropic melt near the I₁-to-I₂ phase transition, a very weak small angle reflection, indicates incipient lamellar-like clustering of the aggregated mesogens. With decreasing temperature the intensity of the small angle reflection increases and in the smectic A phase, the reflection becomes very sharp. In the cubic phase the small angle reflection splits into two peaks which can be indexed with a face-centred cubic (FCC) structure. The deuterium NMR measurements in the isotropic and smectic A phases are indicative of aggregation and an oriented, lamellarlike structure, respectively. In the cubic phase, the collapse of quadrupolar splittings is consistent with an isotropic average of the quadrupole interaction caused by mesogen translational diffusion through a cubic supramolecular structure.