Vibrational spectroscopy of the borate mineral henmilite Ca2Cu[B(OH)4]2(OH)4

Henmilite is a triclinic mineral with the crystal structure consisting of isolated B(OH)4 tetrahedra, planar Cu(OH)4 groups and Ca(OH)3 polyhedra. The structure can also be viewed as having dimers of Ca polyhedra connected to each other through 2B(OH) tetrahedra to form chains parallel to the C axis. The structure of the mineral has been assessed by the combination of Raman and infrared spectra. Raman bands at 902, 922, 951, and 984 cm−1 and infrared bands at 912, 955 and 998 cm−1 are assigned to stretching vibrations of tetragonal boron. The Raman band at 758 cm−1 is assigned to the symmetric stretching mode of tetrahedral boron. The series of bands in the 400–600 cm−1 region are due to the out-of-plane bending modes of tetrahedral boron. Two very sharp Raman bands are observed at 3559 and 3609 cm−1. Two infrared bands are found at 3558 and 3607 cm−1. These bands are assigned to the OH stretching vibrations of the OH units in henmilite. A series of Raman bands are observed at 3195, 3269, 3328, 3396, 3424 and 3501 cm−1 are assigned to water stretching modes. Infrared spectroscopy also identified water and OH units in the henmilite structure. It is proposed that water is involved in the structure of henmilite. Hydrogen bond distances based upon the OH stretching vibrations using a Libowitzky equation were calculated. The number and variation of water hydrogen bond distances are important for the stability off the mineral.

The mineral tooeleite Fe6(AsO3)4SO4(OH)4⋅4H2O – An infrared and Raman spectroscopic study-environmental implications for arsenic remediation

The mineral tooeleite Fe6(AsO3)4SO4(OH)4�4H2O is secondary ferric arsenite sulphate mineral which has environmental significance for arsenic remediation because of its high stability in the regolith. The mineral has been studied by X-ray diffraction (XRD), infrared (IR) and Raman spectroscopy. The XRD result indicates tooeleite can form more crystalline solids in an acid environment than in an alkaline environment. Infrared spectroscopy identifies moderately intense band at 773 cm�1 assigned to AsO3� 3 symmetric stretching vibration. Raman spectroscopy identifies three bands at 803, 758 and 661 cm�1 assigned to the symmetric and antisymmetric stretching vibrations of AsO3� 3 and As-OH stretching vibration respectively. In addition, the infrared bands observed at 1116, 1040, 1090, 981 and 616 cm�1, are assigned to the m3, m1 and m4 modes of SO2� 4 . The same bands are observed at 1287, 1085, 983 and 604 cm�1 in the Raman spectrum. As3d band at binding energy of 44.05 eV in XPS confirms arsenic valence of tooeleite is +3. These characteristic bands in the IR and Raman spectra provide useful basis for identifying the mineral tooeleite.

The molecular structure of matioliite – NaMgAl5(PO4)4(OH)6·2(H2O) : a pegmatite mineral from Minas Gerais, Brazil

Detailed spectroscopic and chemical investigation of matioliite, including infrared and Raman spectroscopy, scanning electron microscopy and electron probe microanalysis has been carried out on homogeneous samples from the Gentil pegmatite, Mendes Pimentel, Minas Gerais, Brazil. The chemical composition is (wt.%): FeO 2.20, CaO 0.05, Na2O 1.28, MnO 0.06, Al2O3 39.82, P2O5 42.7, MgO 4.68, F 0.02 and H2O 9.19; total 100.00. The mineral crystallize in the monoclinic crystal system, C2/c space group, with a = 25.075(1) Å, b = 5.0470(3) Å, c = 13.4370(7) Å, β = 110.97(3)°, V = 1587.9(4) Å3, Z = 4. Raman spectroscopy coupled with infrared spectroscopy supports the concept of phosphate, hydrogen phosphate and dihydrogen phosphate units in the structure of matioliite. Infrared and Raman bands attributed to water and hydroxyl stretching modes are identified. Vibrational spectroscopy adds useful information to the molecular structure of matioliite.

Vibrational spectroscopic characterization of the phosphate mineral anapaite Ca2Fe2+(PO4)2 · 4(H2O)

We have characterized anapaite Ca2Fe2+(PO4)2·4(H2O), a rare Ca and Fe phosphate, using a combination of electron microscopy and vibrational spectroscopy. The mineral occurs in soils and lacustrine sediments and is usually related to the diagenetic process in phosphorous rich sediments. The phosphate anion is characterized by its Raman spectrum with an intense sharp band at 943 cm-1, attributed to the ν1 PO4 3- symmetric stretching mode. Three bands at 992, 1039 and 1071 cm-1 are attributed to ν3 PO4 3-antisymmetric stretching modes. The infrared spectrum of anapaite shows complexity with a series of overlapping bands. Water in the structure of anapaite is observed by OH stretching vibrations at 2777, 3022 and 3176 cm-1 (Raman) and 2744, 3014 and 3096 cm-1 (infrared). The position of these bands provides evidence for the strong hydrogen bonding of water in the anapaite structure and contributes to the stability of the mineral.

2-(4-Aminobenzenesulfonamido)-4,6-dimetylpyrimidin-1-ium 2-carboxy-4,6-dinitrophenolate

In the structure of the of the phenolate salt of the sulfa drug sulfamethazine with 3,5-dinitrosalicylic acid, C12H15N4O2S+ C7H3N2O7-, the dihedral angle between the pyrimidine and phenyl rings of the cation is 59.70(17)\%. Cation--anion hydrogen-bonding interactions involving pyrimidine N+-H...O(carboxyl) and amine N-H...O(carboxyl) pairs give a cyclic R2/2(8) motif while secondary N-H...O hydrogen bonds between the aniline group and both sulfone and nitro O-atom acceptors give a two-dimensional structure extending along (001).

SEM-EDX, Raman and infrared spectroscopic characterization of the phosphate mineral frondelite (Mn2+)(Fe3+)4(PO4)3(OH)5

We have analyzed a frondelite mineral sample from the Cigana mine, located in the municipality of Conselheiro Pena, a well-known pegmatite in Brazil. In the Cigana pegmatite, secondary phosphates, namely eosphorite, fairfieldite, fluorapatite, frondelite, gormanite, hureaulite, lithiophilite, reddingite and vivianite are common minerals in miarolitic cavities and in massive blocks after triphylite. The chemical formula was determined as (Mn0.68, Fe0.32)(Fe3+)3,72(PO4)3.17(OH)4.99. The structure of the mineral was assessed using vibrational spectroscopy. Bands attributed to the stretching and bending modes of PO4 3- and HOPO3 3- units were identified. The observation of multiple bands supports the concept of symmetry reduction of the phosphate anion in the frondelite structure. Sharp Raman and infrared bands at 3581 cm−1 is assigned to the OH stretching vibration. Broad Raman bands at 3063, 3529 and 3365 cm−1 are attributed to water stretching vibrational modes.

Infrared and Raman spectroscopic characterization of the silicate-carbonate mineral carletonite – KNa4Ca4Si8O18(CO3)4(OH,F) H2O

Abstract An assessment of the molecular structure of carletonite a rare phyllosilicate mineral with general chemical formula given as KNa4Ca4Si8O18(CO3)4(OH,F)·H2O has been undertaken using vibrational spectroscopy. Carletonite has a complex layered structure. Within one period of c, it contains a silicate layer of composition NaKSi8O18·H2O, a carbonate layer of composition NaCO3·0.5H2O and two carbonate layers of composition NaCa2CO3(F,OH)0.5. Raman bands are observed at 1066, 1075 and 1086 cm−1. Whether these bands are due to the CO32- ν1 symmetric stretching mode or to an SiO stretching vibration is open to question. Multiple bands are observed in the 300–800 cm−1 spectral region, making the attribution of these bands difficult. Multiple water stretching and bending modes are observed showing that there is much variation in hydrogen bonding between water and the silicate and carbonate surfaces.

Kinetic energy of He atoms in liquid He-4-He-3 mixtures

Deep inelastic neutron scattering measurements on liquid 3He-4He mixtures in the normal phase have been performed on the VESUVIO spectrometer at the ISIS pulsed neutron source at exchanged wave vectors of about q≃120.0Å-1. The neutron Compton profiles J(y) of the mixtures were measured along the T=1.96K isotherm for 3He concentrations, x, ranging from 0.1 to 1.0 at saturated vapor pressures. Values of kinetic energies 〈T〉 of 3He and 4He atoms as a function of x, 〈T〉(x), were extracted from the second moment of J(y). The present determinations of 〈T〉(x) confirm previous experimental findings for both isotopes and, in the case of 3He, a substantial disagreement with theory is found. In particular 〈T〉(x) for the 3He atoms is found to be independent of concentration yielding a value 〈T〉3(x=0.1)≃12K, much lower than the value suggested by the most recent theoretical estimates of approximately 19 K.

Calculation of dose kernels for radiotherapy applications using the GEANT 4 Monte Carlo toolkit

Dose kernels may be used to calculate dose distributions in radiotherapy (as described by Ahnesjo et al., 1999). Their calculation requires use of Monte Carlo methods, usually by forcing interactions to occur at a point. The Geant4 Monte Carlo toolkit provides a capability to force interactions to occur in a particular volume. We have modified this capability and created a Geant4 application to calculate dose kernels in cartesian, cylindrical, and spherical scoring systems. The simulation considers monoenergetic photons incident at the origin of a 3 m x 3 x 9 3 m water volume. Photons interact via compton, photo-electric, pair production, and rayleigh scattering. By default, Geant4 models photon interactions by sampling a physical interaction length (PIL) for each process. The process returning the smallest PIL is then considered to occur. In order to force the interaction to occur within a given length, L_FIL, we scale each PIL according to the formula: PIL_forced = L_FIL 9 (1 - exp(-PIL/PILo)) where PILo is a constant. This ensures that the process occurs within L_FIL, whilst correctly modelling the relative probability of each process. Dose kernels were produced for an incident photon energy of 0.1, 1.0, and 10.0 MeV. In order to benchmark the code, dose kernels were also calculated using the EGSnrc Edknrc user code. Identical scoring systems were used; namely, the collapsed cone approach of the Edknrc code. Relative dose difference images were then produced. Preliminary results demonstrate the ability of the Geant4 application to reproduce the shape of the dose kernels; median relative dose differences of 12.6, 5.75, and 12.6 % were found for an incident photon energy of 0.1, 1.0, and 10.0 MeV respectively.

Recent emergence of dengue virus serotype 4 in French Polynesia results from multiple introductions from other south pacific islands

BACKGROUND: Infection by dengue virus (DENV) is a major public health concern in hundreds of tropical and subtropical countries. French Polynesia (FP) regularly experiences epidemics that initiate, or are consecutive to, DENV circulation in other South Pacific Island Countries (SPICs). In January 2009, after a decade of serotype 1 (DENV-1) circulation, the first cases of DENV-4 infection were reported in FP. Two months later a new epidemic emerged, occurring about 20 years after the previous circulation of DENV-4 in FP. In this study, we investigated the epidemiological and molecular characteristics of the introduction, spread and genetic microevolution of DENV-4 in FP. METHODOLOGY/PRINCIPAL FINDINGS: Epidemiological data suggested that recent transmission of DENV-4 in FP started in the Leeward Islands and this serotype quickly displaced DENV-1 throughout FP. Phylogenetic analyses of the nucleotide sequences of the envelope (E) gene of 64 DENV-4 strains collected in FP in the 1980s and in 2009-2010, and some additional strains from other SPICs showed that DENV-4 strains from the SPICs were distributed into genotypes IIa and IIb. Recent FP strains were distributed into two clusters, each comprising viruses from other but distinct SPICs, suggesting that emergence of DENV-4 in FP in 2009 resulted from multiple introductions. Otherwise, we observed that almost all strains collected in the SPICs in the 1980s exhibit an amino acid (aa) substitution V287I within domain I of the E protein, and all recent South Pacific strains exhibit a T365I substitution within domain III. CONCLUSIONS/SIGNIFICANCE: This study confirmed the cyclic re-emergence and displacement of DENV serotypes in FP. Otherwise, our results showed that specific aa substitutions on the E protein were present on all DENV-4 strains circulating in SPICs. These substitutions probably acquired and subsequently conserved could reflect a founder effect to be associated with epidemiological, geographical, eco-biological and social specificities in SPICs.

2-[(3,3-Dimethylindolin-2-ylidene)methyl]-4-[(3,3-dimethyl-3H-indol-1-ium-2-yl)methylidene]-3-oxocyclobut-1-en-1-olate chloroform disolvate

In the title squaraine dye solvate, C26H24N2O2·2CHCl3, the dye molecule is essentially planar, except for the methyl groups, having a maximum deviation over the 26-membered delocalized bond system of 0.060 (2) Å. It possesses crystallographic twofold rotational symmetry with the indole ring systems adopting a syn conformation. The molecular structure features intramolecular N-HO hydrogen bonds enclosing conjoint S7 ring motifs about one of the dioxocyclobutene O atoms, while the two chloroform solvent molecules are linked to the second O atom through C-HO hydrogen bonds.

Hydrogen bonding in two ammonium salts of 5-sulfosalicylic acid : ammonium 3-carboxy-4-hydroxybenzenesulfonate monohydrate and triammonium 3-carboxy-4-hydroxybenzenesulfonate 3-carboxylato-4-hydroxybenzenesulfonate

The structures of two ammonium salts of 3-carboxy-4-hydroxybenzenesulfonic acid (5-sulfosalicylic acid, 5-SSA) have been determined at 200 K. In the 1:1 hydrated salt, ammonium 3-carboxy-4-hydroxybenzenesulfonate monohydrate, NH4+·C7H5O6S-·H2O, (I), the 5-SSA- monoanions give two types of head-to-tail laterally linked cyclic hydrogen-bonding associations, both with graph-set R44(20). The first involves both carboxylic acid O-HOwater and water O-HOsulfonate hydrogen bonds at one end, and ammonium N-HOsulfonate and N-HOcarboxy hydrogen bonds at the other. The second association is centrosymmetric, with end linkages through water O-HOsulfonate hydrogen bonds. These conjoined units form stacks down c and are extended into a three-dimensional framework structure through N-HO and water O-HO hydrogen bonds to sulfonate O-atom acceptors. Anhydrous triammonium 3-carboxy-4-hydroxybenzenesulfonate 3-carboxylato-4-hydroxybenzenesulfonate, 3NH4+·C7H4O6S2-·C7H5O6S-, (II), is unusual, having both dianionic 5-SSA2- and monoanionic 5-SSA- species. These are linked by a carboxylic acid O-HO hydrogen bond and, together with the three ammonium cations (two on general sites and the third comprising two independent half-cations lying on crystallographic twofold rotation axes), give a pseudo-centrosymmetric asymmetric unit. Cation-anion hydrogen bonding within this layered unit involves a cyclic R33(8) association which, together with extensive peripheral N-HO hydrogen bonding involving both sulfonate and carboxy/carboxylate acceptors, gives a three-dimensional framework structure. This work further demonstrates the utility of the 5-SSA- monoanion for the generation of stable hydrogen-bonded crystalline materials, and provides the structure of a dianionic 5-SSA2- species of which there are only a few examples in the crystallographic literature.

Proton-transfer compounds with 4-amino-N-(4,6-dimethylpyrimidin-2-yl)benzenesulfonamide (sulfamethazine): the structures and hydrogen-bonding in the salts with 5-nitrosalicylic acid and picric acid

The structures of the anhydrous proton-transfer compounds of the sulfa drug sulfamethazine with 5-nitrosalicylic acid and picric acid, namely 2-(4-aminobenzenesulfonamido)-4,6-dimethylpyrimidinium 2-hydroxy-5-nitrobenzoate, C12H15N4O2S(+)·C7H4NO4(-), (I), and 2-(4-aminobenzenesulfonamido)-4,6-dimethylpyrimidinium 2,4,6-trinitrophenolate, C12H15N4O2S(+)·C6H2N3O7(-), (II), respectively, have been determined. In the asymmetric unit of (I), there are two independent but conformationally similar cation-anion heterodimer pairs which are formed through duplex intermolecular N(+)-H...Ocarboxylate and N-H...Ocarboxylate hydrogen-bond pairs, giving a cyclic motif [graph set R2(2)(8)]. These heterodimers form separate and different non-associated substructures through aniline N-H...O hydrogen bonds, one one-dimensional, involving carboxylate O-atom acceptors, the other two-dimensional, involving both carboxylate and hydroxy O-atom acceptors. The overall two-dimensional structure is stabilized by π-π interactions between the pyrimidinium ring and the 5-nitrosalicylate ring in both heterodimers [minimum ring-centroid separation = 3.4580 (8) Å]. For picrate (II), the cation-anion interaction involves a slightly asymmetric chelating N-H...O R2(1)(6) hydrogen-bonding association with the phenolate O atom, together with peripheral conjoint R1(2)(6) interactions between the same N-H groups and O atoms of the ortho-related nitro groups. An inter-unit amine N-H...Osulfone hydrogen bond gives one-dimensional chains which extend along a and inter-associate through π-π interactions between the pyrimidinium rings [centroid-centroid separation = 3.4752 (9) Å]. The two structures reported here now bring to a total of four the crystallographically characterized examples of proton-transfer salts of sulfamethazine with strong organic acids.

A practical comparison of manual and autonomous methods for acoustic monitoring

1. Autonomous acoustic recorders are widely available and can provide a highly efficient method of species monitoring, especially when coupled with software to automate data processing. However, the adoption of these techniques is restricted by a lack of direct comparisons with existing manual field surveys. 2. We assessed the performance of autonomous methods by comparing manual and automated examination of acoustic recordings with a field-listening survey, using commercially available autonomous recorders and custom call detection and classification software. We compared the detection capability, time requirements, areal coverage and weather condition bias of these three methods using an established call monitoring programme for a nocturnal bird, the little spotted kiwi(Apteryx owenii). 3. The autonomous recorder methods had very high precision (>98%) and required <3% of the time needed for the field survey. They were less sensitive, with visual spectrogram inspection recovering 80% of the total calls detected and automated call detection 40%, although this recall increased with signal strength. The areal coverage of the spectrogram inspection and automatic detection methods were 85% and 42% of the field survey. The methods using autonomous recorders were more adversely affected by wind and did not show a positive association between ground moisture and call rates that was apparent from the field counts. However, all methods produced the same results for the most important conservation information from the survey: the annual change in calling activity. 4. Autonomous monitoring techniques incur different biases to manual surveys and so can yield different ecological conclusions if sampling is not adjusted accordingly. Nevertheless, the sensitivity, robustness and high accuracy of automated acoustic methods demonstrate that they offer a suitable and extremely efficient alternative to field observer point counts for species monitoring.