Crystal structures of the co-crystalline adduct 5-(4-bromophenyl)-1,3,4-thiadiazol-2-amine--4-nitrobenzoic acid (1/1) and the salt 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazol-3-ium 2-carboxy-4,6-dinitrophenolate

The structures of the 1:1 co-crystalline adduct C8H6BrN3S . C7H5NO4 (I) and the salt C8H7BrN3S+ C7H3N2O7- (II) from the interaction of 5-(4-bromophenyl)-1,3,4-thiadiazol-2-amine with 4-nitrobenzoic acid and 3,5-dinitrosalicylic acid, respectively, have been determined. The primary inter-species association in both (I) and (II) is through duplex R2/2(8) (N-H...O/O-H...O) or (N-H...O/N-H...O) hydrogen bonds, respectively, giving heterodimers. In (II), these are close to planar [dihedral angles between the thiadiazole ring and the two phenyl rings are 2.1(3)deg. (intra) and 9.8(2)deg. (inter)], while in (I) these angles are 22.11(15) and 26.08(18)deg., respectively. In the crystal of (I), the heterodimers are extended into a one-dimensional chain along b through an amine N-...N(thiadiazole) hydrogen bond but in (II), a centrosymmetric cyclic heterotetramer structure is generated through N-H...O hydrogen bonds to phenol and nitro O-atom acceptors and features, together with the primary R2/2(8) interaction, conjoined R4/6(12), R2/1(6) and S(6) ring motifs. Also present in (I) are pi--pi interactions between thiadiazole rings [minimum ring centroid separation, 3.4624(16)deg.] as well as short Br...O(nitro) interactions in both (I) and (II) [3.296(3)A and 3.104(3)A, respectively].

Crystal structures and hydrogen bonding in the proton transfer salts of nicotine with 3,5-dinitrosalicylic acid and 5-sulfosalicylic acid

The structures of the 1:1 anhydrous salts of nicotine (NIC) with 3,5-dinitrosalicylic acid (DNSA) and 5-sulfosalicylic acid (5-SSA), namely (1R,2S)-1-methyl-2-(3-pyridyl)-1H-pyrrolidin-1-ium 2-carboxy-4,6-dinitrophenolate, C10H15N2+ C7H3N2O7-, (I) and (1R,2S)-1-methyl-2-(3-pyridyl)-1H-pyrrolidin-1-ium 3-carboxy-4-hydroxybenzenesulfonate, C10H15N2+ C7H5O6S-, (II) are reported. The asymmetric units of both (I) and (II) comprise two independent nicotinium cations (C and D) and either two DNSA or two 5-SSA anions (A and B), respectively. One of the DNSA anions shows a 25% rotational disorder in the benzene ring system. In the crystal of (I), inter-unit pyrrolidinium N-H...N(pyridine) hydrogen bonds generate zigzag NIC cation chains which extend along a while the DNSA anions are not involved in any formal inter-species hydrogen bonding but instead form pi--pi associated stacks which parallel the NIC chains along a [ring centroid separation, 3.857(2)A]. Weak C-H...O interactions between chain substructures give an overall three-dimensional structure. With (II), A and B anions form independent zigzag chains with C and D cations, respectively, through carboxylic acid O-H...N(pyridine) hydrogen bonds. These chains, which extend along b are pseudo-centrosymmetrically related and give pi--pi interactions between the benzene rings of anions A and B and the pyridine rings of the NIC cations C and D, respectively [ring centroid separations, 3.6422(19) and 3.7117(19)A]. Present also are weak intermolecular C-H...O hydrogen-bonding interactions between the chains, giving an overall three-dimensional structure.

Two-dimensional hydrogen-bonded polymers in the crystal structures of the ammonium salts of phenoxyacetic acid, (4-fluorophenoxy)acetic acid and (4-chloro-2-methylphenoxy)acetic acid

The structures of the ammonium salts of phenoxyacetic acid, NH4+ C8H6O3- (I), (4-fluorophenoxy)acetic acid NH4+ C8H5FO3- (II) and the herbicidally active (4-chloro-2-methylphenoxy)acetic acid (MCPA), NH4+ C9H8ClO3-. 0.5(H2O) (III) have been determined. All have two-dimensional layered structures based on inter-species ammonium N-H...O hydrogen-bonding associations which give core substructures consisting primarily of conjoined cyclic motifs. Crystals of (I) and (II) are isomorphous with the core comprising R2/1(5), R2/1(4) and centrosymmetric R2/4(8) ring motifs, giving two-dimensional layers lying parallel to (100). In (III), the water molecule of solvation lies on a crystallographic twofold rotation axis and bridges two carboxyl O-atoms in an R4/4(12) hydrogen-bonded motif, creating two R3/4(10) rings which together with a conjoined centrosymmetric R2/4(8) ring incorporating both ammonium cations, generate two-dimensional layers lying parallel to (100). No pi-pi ring associations are present in any of the structures.

5,7-di-N-acetyl-acinetaminic acid: A novel non-2-ulosonic acid found in the capsule of an Acinetobacter baumannii isolate

An Acinetobacter baumannii global clone 1 (GC1) isolate was found to carry a novel capsule biosynthesis gene cluster, designated KL12. KL12 contains genes predicted to be involved in the synthesis of simple sugars, as well as ones for N-acetyl-l-fucosamine (l-FucpNAc) and N-acetyl-d-fucosamine (d-FucpNAc). It also contains a module of 10 genes, 6 of which are required for 5,7-di-N-acetyl-legionaminic acid synthesis. Analysis of the composition of the capsule revealed the presence of N-acetyl-d-galactosamine, l-FucpNAc and d-FucpNAc, confirming the role of fnlABC and fnr/gdr genes in the synthesis of l-FucpNAc and d-FucpNAc, respectively. A non-2-ulosonic acid, shown to be 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-altro-non-2-ulosonic acid, was also detected. This sugar has not previously been recovered from biological source, and was designated 5,7-di-N-acetyl-acinetaminic acid (Aci5Ac7Ac). Proteins encoded by novel genes, named aciABCD, were predicted to be involved in the conversion of 5,7-di-N-acetyl-legionaminic acid to Aci5Ac7Ac. A pathway for 5,7-di-N-acetyl-8-epilegionaminic acid biosynthesis was also proposed. In available A. baumannii genomes, genes for the synthesis of 5,7-di-N-acetyl-acinetaminic acid were only detected in two closely related capsule gene clusters, KL12 and KL13, which differ only in the wzy gene. KL12 and KL13 are carried by isolates belonging to clinically important clonal groups, GC1, GC2 and ST25. Genes for the synthesis of N-acyl derivatives of legionaminic acid were also found in 10 further A. baumannii capsule gene clusters, and three carried additional genes for production of 5,7-di-N-acetyl-8-epilegionaminic acid.

Design and synthesis of a screening library using the natural product scaffold 3-chloro-4-hydroxyphenylacetic acid

The fungal metabolite 3-chloro-4-hydroxyphenylacetic acid (1) was utilized in the generation of a unique drug-like screening library using parallel solution-phase synthesis. A 20-membered amide library (3–22) was generated by first converting 1 to methyl (3-chloro-4-hydroxyphenyl)acetate (2), then reacting this scaffold with a diverse series of primary amines via a solvent-free aminolysis procedure. The structures of the synthetic analogues (3–22) were elucidated by spectroscopic data analysis. The structures of compounds 8, 12, and 22 were confirmed by single X-ray crystallographic analysis. All compounds were evaluated for cytotoxicity against a human prostate cancer cell line (LNCaP) and for antiparasitic activity toward Trypanosoma brucei brucei and Plasmodium falciparum and showed no significant activity at 10 μM. The library was also tested for effects on the lipid content of LNCaP and PC-3 prostate cancer cells, and it was demonstrated that the fluorobenzyl analogues (12–14) significantly reduced cellular phospholipid and neutral lipid levels.

Characterization of the sulphate mineral coquimbite, a secondary iron sulphate from Javier Ortega mine, Lucanas Province, Peru – Using infrared, Raman spectroscopy and thermogravimetry

The mineral coquimbite has been analysed using a range of techniques including SEM with EDX, thermal analytical techniques and Raman and infrared spectroscopy. The mineral originated from the Javier Ortega mine, Lucanas Province, Peru. The chemical formula was determined as ðFe3þ 1:37; Al0:63ÞP2:00ðSO4Þ3 9H2O. Thermal analysis showed a total mass loss of 73.4% on heating to 1000 C. A mass loss of 30.43% at 641.4 C is attributed to the loss of SO3. Observed Raman and infrared bands were assigned to the stretching and bending vibrations of sulphate tetrahedra, aluminium oxide/hydroxide octahedra, water molecules and hydroxyl ions. The Raman spectrum shows well resolved bands at 2994, 3176, 3327, 3422 and 3580 cm 1 attributed to water stretching vibrations. Vibrational spectroscopy combined with thermal analysis provides insight into the structure of coquimbite.

Vibrational spectroscopic characterization of the sulphate-carbonate mineral burkeite: Implications for evaporites

Burkeite formation is important in saline evaporites and in pipe scales. Burkeite is an anhydrous sulphate-carbonate with an apparent variable anion ratio. Such a formula with two oxyanions lends itself to vibrational spectroscopy. Two symmetric sulphate stretching modes are observed, indicating at least at the molecular level the nonequivalence of the sulphate ions in the burkeite structure. The strong Raman band at 1065 cm−1 is assigned to the carbonate symmetric stretching vibration. The series of Raman bands at 622, 635, 645, and 704 cm−1 are assigned to the ν4 sulphate bending modes. The observation of multiple bands supports the concept of a reduction in symmetry of the sulphate anion from T d to C 3v or even C 2v.

Investigation of the effects of the fatty acid profile on fuel properties using a Multi-Criteria Decision Analysis

The structural features of fatty acids in biodiesel, including degree of unsaturation, percentage of saturated fatty acids and average chain length, influence important fuel properties such as cetane number, iodine value, density, kinematic viscosity, higher heating value and oxidation stability. The composition of fatty acid esters within the fuel should therefore be in the correct ratio to ensure fuel properties are within international biodiesel standards such as ASTM 6751 or EN 14214. This study scrutinises the influence of fatty acid composition and individual fatty acids on fuel properties. Fuel properties were estimated based on published equations, and measured according to standard procedure ASTM D6751 and EN 14214 to confirm the influences of the fatty acid profile. Based on fatty acid profile-derived calculations, the cetane number of the microalgal biodiesel was estimated to be 11.6, but measured 46.5, which emphasises the uncertainty of the method used for cetane number calculation. Multi-criteria decision analysis (MCDA), PROMETHEE-GAIA, was used to determine the influence of individual fatty acids on fuel properties in the GAIA plane. Polyunsaturated fatty acids increased the iodine value and had a negative influence on cetane number. Kinematic viscosity was negatively influenced by some long chain polyunsaturated fatty acids such as C20:5 and C22:6 and some of the more common saturated fatty acids C14:0 and C18:0. The positive impact of average chain length on higher heating value was also confirmed in the GAIA plane

Limitations of a laboratory scale model in predicting optimal pilot scale conditions for dilute acid pretreatment of sugarcane bagasse

Pilot and industrial scale dilute acid pretreatment data can be difficult to obtain due to the significant infrastructure investment required. Consequently, models of dilute acid pretreatment by necessity use laboratory scale data to determine kinetic parameters and make predictions about optimal pretreatment conditions at larger scales. In order for these recommendations to be meaningful, the ability of laboratory scale models to predict pilot and industrial scale yields must be investigated. A mathematical model of the dilute acid pretreatment of sugarcane bagasse has previously been developed by the authors. This model was able to successfully reproduce the experimental yields of xylose and short chain xylooligomers obtained at the laboratory scale. In this paper, the ability of the model to reproduce pilot scale yield and composition data is examined. It was found that in general the model over predicted the pilot scale reactor yields by a significant margin. Models that appear very promising at the laboratory scale may have limitations when predicting yields on a pilot or industrial scale. It is difficult to comment whether there are any consistent trends in optimal operating conditions between reactor scale and laboratory scale hydrolysis due to the limited reactor datasets available. Further investigation is needed to determine whether the model has some efficacy when the kinetic parameters are re-evaluated by parameter fitting to reactor scale data, however, this requires the compilation of larger datasets. Alternatively, laboratory scale mathematical models may have enhanced utility for predicting larger scale reactor performance if bulk mass transport and fluid flow considerations are incorporated into the fibre scale equations. This work reinforces the need for appropriate attention to be paid to pilot scale experimental development when moving from laboratory to pilot and industrial scales for new technologies.

Cortisol and dehydroepiandrosterone-sulphate levels correlate with symptom severity in first-episode psychosis

Dehydroepiandrosterone (DHEA) and its sulphate form (DHEA) are neuroactive steroids with antiglucocorticoid properties. An imbalance in the ratio of cortisol to DHEA(S) has been implicated in the pathophysiology of stress-related psychiatric disorders. This study prospectively investigated circulating cortisol, DHEAS and their ratio in first-episode psychosis (FEP) patients compared to healthy controls, and their relationship to perceived stress, psychotic, negative and mood symptoms. METHODS: Blood cortisol and DHEAS levels were obtained in 39 neuroleptic-naïve or minimally-treated FEP patients and 25 controls. Twenty-three patients and 15 controls received repeat assessments after 12 weeks. Perceived stress was assessed using the Perceived Stress Scale and symptoms were assessed in patients using standard rating scales. RESULTS: At baseline, no differences were observed in cortisol, DHEAS or the cortisol/DHEAS ratio between patients and controls. There were also no group differences in the change in these biological variables during the study period. Within FEP patients, decreases in cortisol and the cortisol/DHEAS ratio over time were directly related to the improvement in depression (r = 0.45; p = 0.031, r = 0.52; p = 0.01), negative (r = 0.51; p = 0.006, r = 0.55; p = 0.008) and psychotic symptoms (cortisol only, r = 0.53; p = 0.01). Perceived stress significantly correlated with DHEAS (r = 0.51; p = 0.019) and the cortisol/DHEAS ratio (r = -0.49; p = 0.024) in controls, but not patients, possibly reflecting an impaired hormonal response to stress in FEP patients. CONCLUSIONS: These findings further support the involvement of the stress system in the pathophysiology of psychotic disorders, with implications for treatment strategies that modulate these neurosteroids.

A Raman and infrared spectroscopic study of the sulphate mineral aluminite Al2(SO4)(OH)4·7H2O

The mineral aluminite has been studied using a number of techniques, including scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDX) and Raman and infrared spectroscopy. Raman spectroscopy identifies multiple sulphate symmetric stretching modes in line with the three sulphate crystallographically different sites. Raman spectroscopy also identifies a low intensity band at 1069 cm−1 which may be attributed to a carbonate symmetric stretching mode, indicating the presence of thaumasite. The observation of multiple bands in this ν4 spectral region offers evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 3588 cm−1 is assigned to the OH unit stretching vibration and the broad feature at around 3439 cm−1 to water stretching bands. Water stretching vibrations are observed at 3157, 3294, 3378 and 3439 cm−1. Vibrational spectroscopy enables an assessment of the molecular structure of aluminite to be made.

The structures of the isomorphous potassium and rubidium salts of 4-nitrobenzoic acid and an overview of the metal complex stereochemistries of the alkali metal salt series with this ligand

The structures of the isomorphous potassium and rubidium polymeric coordination complexes with 4-nitrobenzoic acid, poly[mu2-aqua-aqua-mu3-(4-nitrobenzoato)-potassium], [K(C7H4N2O2)(H2O)2]n, (I) and poly[mu3-aqua-aqua-mu5-(4-nitrobenzoato)-rubidium], [Rb(C7H4N2O2)(H2O)2]n, (II) have been determined. In (I) the very distorted KO6 coordination sphere about the K+ centres in the repeat unit comprise two bridging nitro O-atom donors, a single bridging carboxyl O-atom donor and two water molecules, one of which is bridging. In the the Rb complex (II), the same basic MO6 coordination is found in the repeat unit but is expanded to RbO9 through a slight increase in the accepted Rb-O bond length range and includes an additional Rb-O(carboxyl) bond, completing a bidentate O,O'-chelate interaction, and additional bridging Rb-Onitro) and Rb-O(water) bonds. The comparative K-O and Rb-O bond length ranges are 2.738(3)-3.002(3)Ang. (I) and 2.884(2)-3.182(2)Ang. (II). The structure of (II) is also isomorphous as well as isostructural with the known structure of the nine-coordinate caesium 4-nitrobenzoate analogue, [Cs(C7H4N2O~2~)(H~2~O)2]n, (III) in which the Cs---O range is 3.047(4)-3.338(4)Ang. In all three complexes, common basic polymeric extensions are found, including two different centrosymmetric bridging interactions through both water and nitro groups as well as extensions along c through the p-related carboxyl group, giving a two-dimensional structure in (I). In (II) and (III), three-dimensional structures are generated through additional bridges through the nitro and water O-atoms. In all structures, both water molecules are involved in similar intra-polymer O-H...O hydrogen-bonding interactions to both carboxyl as well as water O-atom acceptors. A comparison of the varied coordination behaviour of the full set of Li-Cs salts with 4-nitrobenzoic acid is also made.

Instant coffee with high chlorogenic acid levels protects humans against oxidative damage of macromolecules

Scope: Coffee is among the most frequently consumed beverages. Its consumption is inversely associated to the incidence of diseases related to reactive oxygen species; the phenomenon may be due to its antioxidant properties. Our primary objective was to investigate the impact of consumption of a coffee containing high levels of chlorogenic acids on the oxidation of proteins, DNA and membrane lipids; additionally, other redox biomarkers were monitored in an intervention trial. Methods and results: The treatment group (n=36) consumed instant coffee co-extracted from green and roasted beans, whereas the control consumed water (800 mL/P/day, 5 days). A global statistical analysis of four main biomarkers selected as primary outcomes showed that the overall changes are significant. 8-Isoprostaglandin F2α in urine declined by 15.3%, 3-nitrotyrosine was decreased by 16.1%, DNA migration due to oxidized purines and pyrimidines was (not significantly) reduced in lymphocytes by 12.5 and 14.1%. Other markers such as the total antioxidant capacity were moderately increased; e.g. LDL and malondialdehyde were shifted towards a non-significant reduction. Conclusion: The oxidation of DNA, lipids and proteins associated with the incidence of various diseases and the protection against their oxidative damage may be indicative for beneficial health effects of coffee.

A comprehensive mechanistic kinetic model for dilute acid hydrolysis of switchgrass cellulose to glucose, 5-HMF and levulinic acid

Switchgrass was treated by 1% (w/w) H₂SO₄in batch tube reactors at temperatures ranging from 140–220°C for up to 60 minutes. In this study, release patterns of glucose, 5-hydroxymethylfurfural (5-HMF), and levulinic acid from switchgrass cellulose were investigated through a mechanistic kinetic model. The predictions were consistent with the measured products of interest when new parameters reflecting the effects of reaction limitations, such as cellulose crystallinity, acid soluble lignin–glucose complex (ASL–glucose) and humins that cannot be quantitatively analyzed, were included. The new mechanistic kinetic model incorporating these parameters simulated the experimental data with R² above 0.97. Results showed that glucose yield was most sensitive to variations in the parameter regarding the cellulose crystallinity at low temperatures (140–180°C), while the impact of crystallinity on the glucose yield became imperceptible at elevated temperatures (200–220 °C). Parameters related to the undesired products (e.g. ASL–glucose and humins) were the most sensitive factors compared with rate constants and other additional parameters in impacting the levulinic acid yield at elevated temperatures (200–220°C), while their impacts were negligible at 140–180°C. These new findings provide a more rational explanation for the kinetic changes in dilute acid pretreatment performance and suggest that the influences of cellulose crystallinity and undesired products including ASL–glucose and humins play key roles in determining the generation of glucose, 5-HMF and levulinic acid from biomass-derived cellulose.

Substrate effects in the supramolecular assembly of 1,3,5-benzene tricarboxylic acid on graphite and graphene

The behavior of small molecules on a surface depends critically on both molecule–substrate and intermolecular interactions. We present here a detailed comparative investigation of 1,3,5-benzene tricarboxylic acid (trimesic acid, TMA) on two different surfaces: highly oriented pyrolytic graphite (HOPG) and single-layer graphene (SLG) grown on a polycrystalline Cu foil. On the basis of high-resolution scanning tunnelling microscopy (STM) images, we show that the epitaxy matrix for the hexagonal TMA chicken wire phase is identical on these two surfaces, and, using density functional theory (DFT) with a non-local van der Waals correlation contribution, we identify the most energetically favorable adsorption geometries. Simulated STM images based on these calculations suggest that the TMA lattice can stably adsorb on sites other than those identified to maximize binding interactions with the substrate. This is consistent with our net energy calculations that suggest that intermolecular interactions (TMA–TMA dimer bonding) are dominant over TMA–substrate interactions in stabilizing the system. STM images demonstrate the robustness of the TMA films on SLG, where the molecular network extends across the variable topography of the SLG substrates and remains intact after rinsing and drying the films. These results help to elucidate molecular behavior on SLG and suggest significant similarities between adsorption on HOPG and SLG.