pinecone/core-2020-05-10-deduplication huggingface dataset:
Vibrational spectra and normal coordinate analysis of CF 3 OF and CF 3 OCl

The IR spectra (1400 cm −1  to 160 cm −1 ) of the gases at ambient temperature and the Raman spectra (below 1400 cm −1 ) of the liquids near −196°C are reported for CF 3 OF and CF 3 OCl. All fundamentals are assigned under  C   s   symmetry and the results of a normal coordinate analysis are presented. The assignments of Smardzewski and Fox are adopted with one exception for both CF 3 OF and CF 3 OCl: the CF 3  rock of  A ″ symmetry is assigned near 430 cm −1  and the two bands between 200 cm −1  and 300 cm −1  are assigned to an  A ′ fundamental, involving CF 3  rocking and COX bending and a Δ ν =2 transition in the CF 3  torsion. An extra band at 548 cm −1  in the Raman spectrum of liquid CF 3  COl near −196°C is assigned to a CF 3 OCl ⃛Cl 2  complex. The values of the force constants  d (OX) for CF 3 OX molecules are suggested to be near those for X 2 O molecules. More than half the normal modes of  A ′ symmetry show extensive mixing of symmetry coordinates. In some of these cases the symmetry coordinate for which the normal mode is named is the largest but not the dominant contributor to the potential energy distribution, while in others this symmetry coordinate is not even the largest contributor to the potential energy distribution. No normal modes of  A ′ symmetry are present in which ν(CO), δ s (CF 3 ), δ(COX), or δ(CF 3 ) symmetry coordinates are dominant, and the mode conventionally labeled as  v (CO) should be labeled as ν s (CF 3 ). For the remaining  A ′ normal modes and all the  A ″ normal modes, the symmetry coordinate for which the normal mode is named is dominant in the potential energy distribution
Inverse Raman spectroscopy of bilirubin and its ditauride

The inverse Raman spectrum of bilirubin and bilirubin ditauride were measured under pre‐resonant conditions. Spectra in chloroform and dimethyl sulfoxide were assigned by comparison with model compounds and on the basis of the known effects of the solvents on the internal hydrogen bonding in bilirubin. The band assignments were used to interpret the spectra of bilirubin ditauride in aqueous solution. Evidence is presented for strong hydrogen bonding to the pyrrole NH bonds and to the lactam rings. It is proposed that hydrogen bonding to water is facilitated by photoactivation and, in turn, stabilizes photohiliruhin
Characterization of the flavin–protein interaction in  L ‐Lactate oxidase and old yellow enzyme by resonance inverse Raman spectroscopy

Resonance inverse Raman spectroscopy was used to examine the interactions between the flavin and surounding protein in  L ‐lactate oxidase (from  Mycobacterium smegmatis ) and Old Yellow Enzyme (from brewer's bottom yeast). Spectra were taken of the enzymes both free and bound to various ligands. For  L ‐lactate oxidase, the ligands consisted of substrate analogs (acetate, propionate) and inorganic anions (phosphate, sulfate and nitrate). For the inorganic anions, the expected attenuation with detuning was not observed for several bands which are associated with flavin rings II and III. This effect appears to be due to a disruption of ring stacking between the uracil–pyrazine end of the flavin moiety and an aromatic amino acid. A shift in the 1232 cm −1  band and changes in the bandwidths of bands in the 1450–1600 cm −1  region indicate minor reorganization of the hydrogen bonding structure around the isoalloxazine on ligand binding.  For Old Yellow Enzyme, the ligand was chloride. Chloride caused a slight change to the Raman spectrum, indicative of decreased hydrogen bonding to the flavin
Vibrational studies of the disulfide group in proteins. VII. Normal mode analysis of the Raman spectra of erabutoxin, γ‐II crystallin and immunoglobulin

Normal mode calculations have been made on the known structures of disulfide bridges in erabutoxin b, a form of γ‐II crystallin, and fragments (Fab, variable‐domain of Bence‐Jones proteins) of immunoglobulins. Previously obtained Raman spectra of these molecules are analyzed in terms of general correlations derived from normal mode calculations and also the results of calculations on these particular structures. This results in more specific conclusions about these disulfide bridge structures and their changes than was possible on the basis of previous empirical correlations
Effects of vinyl substitutions on resonance Raman spectra of (bacterio)chlorophylls

Soret resonance and Qy preresonance Raman spectra are reported and compared for a series of (bacterio)chlorophylls. Chlorophyll a, 2-acetylchlorophyll a, bacteriochlorophyll a and 2-vinylbacteriochlorophyll a were studied in the non-protic solvent tetrahydrofuran. These experiments were designed to identify Raman bands corresponding to the stretching mode(s) of the vinyl group at the C-2 position of ring I of chlorophyll a and 2-vinylbacteriochlorophyll a, and to ascertain whether additional bands corresponding to Ca Cm and/or Cb Cb vibrations could be observed in the 1615-1660 cm-1 region. Raman spectra of chlorophyll a and 2-vinylbacteriochlorophyll a exhibit a 1625 cm-1 band, which is absent from the Raman spectra of 2-acetylchlorophyll a and bacteriochlorophyll a. It is assigned to the vC2a C2b mode of the vinyl group. No other band can be definitively assigned to any mode predominantly arising from vinyl motions. The acetyl-containing molecules 2-acetylchlorophyll a and bacteriochlorophyll a give rise to a ca. 1070 cm-1 band, which appears to be related to the presence of the acetyl substituent. The 1615-1660 cm-1 region of the Raman spectra of all four derivatives did not contain any additional band which could be ascribed to modes involving the vCa Cm and/or Cb Cb coordinates.
Raman spectroscopy of phosphates of the variscite mineral group

Raman spectra of phosphates of the variscite mineral group, namely strengite, variscite, metavariscite and phosphosiderite, were obtained at 298 and 77 K using a thermal stage and complemented with selected infrared data using a diamond attenuated total reflection cell. Multiple phosphate stretching bands are observed. Bands for strengite at 1006, 1012 and 1026 cm-1 at 298 K and at 997, 1006, 1014 and 1027 cm-1 at 77 K are observed. Variscite is characterized by PO stretching vibrations at 1023, 1005 and 938 cm-1 and phosphosiderite by bands at 1009 and 993 cm-1. These minerals are readily identified by their Raman spectrum both in the PO stretching region and in the low-wavenumber region. Multiple bands attributed to the bending modes of PO4 are identified for each of the minerals. A model is proposed involving non-hydrogen-bonded PO4 and strongly hydrogen-bonded PO4 units together with [Al or Fe(OH)2]+ ·(H2PO4)2--type species. Raman spectroscopy shows that at the molecular level multiple species of phosphate anions exist for the variscite phosphate minerals
A comparison of the Raman spectra of natural and synthetic K and Na-jarosites at 298 and 77 K

Raman spectroscopy at 298 and 77 K has been used to characterise synthetic and natural jarosites of formula Mn(Fe 3+)6(SO4)4(OH)12 where M is K or Na.  The natural jarosites are characterised by a well define hydroxyl stretching pattern in contrast to that of the synthetic jarosites. This difference is attributed to differences in hydrogen bonding in the mineral. Multiple Raman OH stretching bands are indicative of non-equivalent OH units in the structure. Jarosites are characterised by an intense sharp band between 1007 and 1010 cm-1attributed to the sulphate symmetric stretching mode.  The band width for K-jarosite is 4.4 cm-1 at 298 K and 3.6 cm-1 at 77 K in comparison to the values for synthetic jarosite  of 10.0 (298 K) and 7.3 cm-1 (77 K).  Differences in the spectra between the natural and synthetic jarosites are found. Reasons for these differences in the spectra are provided
Thermo-Raman spectroscopic study of the uranium mineral sabugalite

The changes in the structure of sabugalite have been undertaken using thermo-Raman and infrared spectroscopy based upon the results of thermogravimetric analysis. Two Raman bands are observed at 835 and 830 cm-1 assigned to the (UO2)2+ stretching vibrations resulting from the non-equivalence of the uranyl bonds (UO2)2+. These bands give calculated U-O bond lengths of 1.773 and 1.7808 Å.  A low intensity band is observed at 895 cm-1 assigned to the ν3 antisymmetric stretching vibration of (UO2)2+ units.  Five bands are observed in the 950 to 1050 cm-1 region in the Raman spectrum of sabugalite and are assigned to the ν3 antisymmetric stretching vibration of (PO4)3-  units.  Changes in the Raman spectra reflect changes in the structure of sabugalite as dehydration occurs.  No (PO4)3-  symmetric stretching mode is observed. This result is attributed to the non-equivalence of the PO bonds in the PO4 units. The PO4 vibrations were not affected by dehydration.  Thermo-Raman spectroscopy proved to be a very powerful technique for the study of the changes in the structure of sabugalite during dehydration
Raman spectroscopy of hydrotalcites with sulphate, molybdate and chromate in the interlayer

Raman microscopy has been used to characterize the interlayer anions in synthesized hydrotalcites of formula Mg6Al2(OH)16(XO4).4H2O where X is S or Mo or Cr. The Raman spectroscopy shows that both the chromate and molybdate anions are not polymerised in the hydrotalcite interlayer. This lack of polymerisation is attributed to the effect of pH during synthesis. A model of bonding is proposed for the interlayer anions based upon the observation of two symmetric stretching modes and symmetry lowering of the chromate, molybdate and sulphate anions.  Two types of anions are present hydrated and hydroxyl surface bonded
Raman spectroscopy of beaverite and plumbojarosite

Raman spectroscopy has been used to characterise the compound of formula Pb(Fe 3+,Cu2+)3(SO4)2(OH)6 equivalent to synthetic beaverite, one of the jarosite subgroup minerals.  The mineral is characterised by multiple OH stretching vibrations attributed to non-equivalent OH units in the structure.  Multiple vibrations are observed for the  stretching vibrations indicating the non-equivalence of the sulphate units in the structure.  This multiplicity is also reflected in the ν2 and ν4 bending modes. The Raman spectrum of beaverite is significantly different from that of plumbojarosite for which multiple bands are not observed
Molecular structure of the uranyl silicates : a Raman spectroscopic study

Raman spectroscopy has been used to study the molecular structure of a series of selected uranyl silicate minerals including uranophane, sklodowskite, cuprosklodowskite, boltwoodite and kasolite.  Raman spectra clearly show well resolved bands in the 750 to 800 cm-1 region and in the 950 to 1000 cm-1 region assigned to the ν1 modes of the (UO2)2+ units and to the (SiO4)4- tetrahedra.  Sets of Raman bands in the 200 to 300 cm-1 region are assigned to ν2 δ (UO2)2+ and UO ligand vibrations.  Multiple bands indicate the non-equivalence of the UO bonds and the lifting of the degeneracy of ν2 δ (UO2)2+ vibrations. The (SiO4)4- tetrahedral are characterized by bands in the 470 to 550 cm-1 and in the 390 to 420 cm-1 region. These bands are attributed to the ν4 and ν2 (SiO4)4- bending modes.  The minerals show characteristic OH stretching bands in the 2900 to 3500 cm-1 and 3600 to 3700 cm-1 region ascribed to water stretching and SiOH stretching vibrations.  The high wavenumber position of the δH2O bands indicate strong hydrogen bonding of water in these uranyl silicates. Bands in the 1400 to 1550 cm-1 region are attributed to δSiOH modes.  The Raman spectroscopy of uranyl silicate minerals enabled separation of the bands attributed to distinct vibrational units. This enabled definitive assignment of the bands. The spectra are analysed in terms of the molecular structure of the minerals
Raman spectroscopy on cubic and hexagonal SrMnO$_3$

We report on the first optical characterization of both cubic and hexagonal
SrMnO$_3$. Room-temperature Raman spectra collected by means of a micro-Raman
spectrometer are shown. The spectrum of the cubic compound is characterized by
weak and broad bands in agreement with group-theory which predicts no
Raman-active phonons for this compound. On the other hand, the spectrum of the
hexagonal compound shows six narrow peaks ascribed to one-phonon processes. A
complete polarization analysis of the spectra collected from a single
crystallite allows us to completely assign the symmetries of the six observed
peaks. Atomic displacements for each phonon peaks are also proposed.Comment: 5 pages, 5 figures, 3 tables, submitted to Journal of Raman
  Spectroscop
Raman spectroscopy of three polymorphs of BiVO4: clinobisvanite, dreyerite and pucherite, with comparisons to (VO4)3-bearing -minerals: namibite, pottsite and schumacherite

Both Raman and infrared spectroscopy have been used to characterise the three phase related minerals dreyerite (tetragonal BiVO4 ), pucherite (orthorhombic BiVO4) and clinobisvanite (monoclinic BiVO4 ) and a comparison of the spectra is made with that of the minerals namibite (Cu(BiO2)VO4(OH)), schumacherite ((Bi3O(OH)(VO4)2) and pottsite (PbBiH(VO4)2.2H2O).  Pucherite, clinobisvanite and namibite are characterised by VO4 stretching vibrations at 872, 824 and 846 cm-1.  The Raman spectrum of dreyerite shows complexity in the 750 to 950 cm-1 region with two intense bands at 836 and 790 cm-1 assigned to the symmetric and antisymmetric VO4 modes. The minerals schumacherite and pottsite are characterised by bands at 846 and 874 cm-1.  In both the infrared and Raman spectra bands are observed in the 1000- 1100 cm-1 region which are attributed to the antisymmetric stretching modes.  The Raman spectra of the low wavenumber region are complex. Bands are identified in the 328 to 370 cm-1 region and in the 404 to 498 cm-1 region and are assigned to the ν2 and ν4 bending modes. The minerals namibite and schumacherite are characterised by intense bands at 3514 and 3589 cm-1 assigned to the symmetric stretching vibrations of the OH units.  Importantly Raman spectroscopy enables new insights into the chemistry of these bismuth vanadate minerals.  Raman spectroscopy enables the identification of the bismuth vanadate minerals in mineral matrices where paragenetic relationships exist between the minerals
Raman spectroscopy of hydrotalcites with phosphate in the interlayer- implications for the removal of phosphate from water

Hydrotalcites with phosphate in the interlayer were prepared at different pH. At pH >11.0 (PO4)3- was the intercalated ionic species whereas at pH < 11.0 a mixture of (PO4)3- and (HPO4)2- ions was intercalated.  Powder X-ray diffraction shows the hydrotalcite formed at pH 9.5 is poorly diffracting with a d-spacing of 11.9; whereas the d(003) spacing for the phosphate interlayered hydrotalcite formed at pH 11.9 and 12.5 were 8.0 and 7.9 Å.  The addition of a thermally activated ZnAl-HT to a phosphate solution resulted in the uptake of the phosphate and the reformation of the hydrotalcite. Raman spectroscopy of the phosphate interlayered  hydrotalcites shows the interlayered anion is pH dependent and only above pH 11.9 is the orthophosphate anion intercalated. At lower pH the monohydrogen phosphate anion is intercalated.  \ud
Raman spectroscopy shows that upon addition of the thermally activated hydrotalcite to an aqueous phosphate solution results in the uptake of phosphate anion from the solution
A Raman spectroscopic study of the uranyl selenite mineral haynesite

The mineral haynesite, a uranyl selenite, has been characterised by Raman spectroscopy at 298 and 77 K.  Two bands at 811.5 and 800.2 cm-1 are assigned to the symmetric stretching modes of the (UO2)2+  and (SeO3)2-  units respectively.  These values give calculated U-O bond lengths of  1.799 and/or 1.801 Å. The broad band at 861.8 cm-1 is assigned to the ν3 antisymmetric stretching mode of the (UO2)2+ (calculated U-O bond length 1.813 Å).   Additional bands are observed in the 77 K spectrum. In the spectroscopy of selenite compounds the position of the antisymmetric stretching vibration occurs at lower wavenumbers than the symmetric stretching mode and thus the band at 746.6 cm-1 is attributed to the ν3 antisymmetric stretching vibration of the (SeO3)2-  units.  The ν4 and the ν2 vibrational modes of the (SeO3)2-  units are observed at 418.5 cm-1 and 472.1 cm-1. Bands observed at 278.3, 257.3 and 218.8 cm-1 are assigned to OUO bending vibrations
A Raman spectroscopic study of the uranyl phosphate mineral parsonsite

The mineral parsonsite with samples from The Ranger Uranium Mine, Australia and La Faye Mine, Grury, Saone-et-Loire, Burgundy, France has been characterised by Raman spectrocopy at 298 and 77 K and complemented with infrared spectroscopy. Two Raman bands close to 807 and 796 cm-1 are attributed to the ￮1 (UO2)2+ symmetric stretching modes, whilst two bands close to 953 or 945 cm-1 and 863-873 cm-1 are assigned to the  ￮3 (UO2)2+ antisymmetric stretching vibrations. Four or five bands (953, 926, 910, 883 cm-1) are observed in the infrared spectrum in this region . Bands at 965-967 and 972 cm-1 are assigned to the ￮1 (PO4)3- symmetric stretching modes and bands that are observed in the 987 to 1078 cm-1 to the ￮3 (PO4)3- antisymmetric stretching modes. Bands at 465, 439, 406, 394 cm-1 (298 K) and 466, 442, 405, 395 cm-1 (77 K) are assigned to the split doubly degenerate ￮2 (PO4)-3 bending vibrations. Bands of very low intensity at 609, 595, 591, 582, 560 and 540 cm-1 are attributed to the split triply degenerate ￮4 (PO4)-3 bending modes. Bands observed at wavenumbers lower than 300 cm-1 are connected with the split ￮2 (￤) (UO2)2+ bending, ￮ (U-Oligand), ￤ (U-Oligand), and lattice vibrations. U-O bond lengths in uranyl are calculated frm the Raman and infrared spectra  which are in agreement with those from available X-ray single crystal structure analysis of parsonsite. Short comment is given to the water content and possibility of a hydrogen bonding network in parsonsite crystal structure
A Raman spectroscopic study of selected minerals of the rosasite group

Minerals in the rosasite mineral group namely rosasite, glaucosphaerite, kolwezite, mcguinnessite, nullaginite and pokrovskite have been studied by Raman spectroscopy at 298 and 77 K and complimented with infrared spectroscopy. The spectral patterns for the minerals rosasite, glaucosphaerite, kolwezite and mcguinnessite are similar to that of malachite implying the structure is the same as malachite i.e. monoclinic. A comparison is made with the spectra of malachite. The symmetry of the carbonate anion in the rosasite mineral group is C2v or Cs and is composition dependent. Two (CO3)2- symmetric stretching modes are observed for the rosasite minerals at 1060 and 1090 cm-1.   Two hydroxyl stretching modes are observed for the rosasite mineral group. The position of these bands is determined to be a function of the hydrogen bond lengths. Hydrogen bond distances for rosasite are calculated as 2.867, 2.799 and 2.780 Å whereas for pokrovskite the distances are 3.280 and 2.999 Å. The effect of lowering the temperature from ambient to 77 K results in a decrease of the hydrogen bond distances by 5%.  Multiple Raman bands are observed in the 800 to 850 cm-1 and the 720 to 750 cm-1 regions and are attributed to ν2 and ν4 bending modes confirming the reduction of the carbonate anion in the rosasite structure
Raman spectroscopic study of the heterogeneity of microcolonies of a pigmented bacterium

Small colonies (90 – 350 μm in diameter) of the pigmented halophilic bacterium Halobacterium salinarium have been studied by Raman microspectroscopy using excitation at 632.8 nm. The Raman spectra were dominated by bands due to carotene compounds. The intensity of the pigment bands varied across the diameter of the colonies in a way that suggested the presence of concentric rings of higher pigment concentration. Although the colonies were grown in a transparent incubator in an open laboratory, it was demonstrated that the rings were not a result of the diurnal variation of light and dark. These results support a proposed model relating cell motility and cell concentration
Raman spectroscopy of the borosilicate mineral ferroaxinite

Raman spectroscopy, complemented by infrared spectroscopy has been used to characterise the ferroaxinite minerals of theoretical formula Ca2Fe2+Al2BSi4O15(OH),  a ferrous aluminium  borosilicate.  The Raman spectra are complex but are subdivided into sections based upon the vibrating units. The Raman spectra are interpreted in terms of the addition of borate and silicate spectra. Three characteristic bands of ferroaxinite are observed at 1082, 1056 and 1025 cm-1 and are attributed to BO4 stretching vibrations.   Bands at 1003, 991, 980 and 963 cm-1 are assigned to SiO4 stretching vibrations. Bands are found in these positions for each of the ferroaxinites studied. No Raman bands were found above 1100 cm-1 showing that ferroaxinites contain only tetrahedral boron. The hydroxyl stretching region of ferroaxinites is characterised by a single Raman band between 3368 and 3376 cm-1, the position of which is sample dependent.  Bands for ferroaxinite at 678, 643, 618, 609, 588, 572, 546 cm-1 may be attributed to the ν4 bending modes and the three bands at 484, 444 and 428 cm-1 may be attributed to the ν2 bending modes of the (SiO4)2-
A Raman spectroscopic study of humite minerals

Raman spectroscopy has been used to study the structure of the humite mineral group ((A2SiO4)n - A(OH, F)2 where n represents the number of olivine and brucite layers in the structure and is 1,2,3 or 4 and A2+ is Mg, Mn, Fe or some mix of these cations). The humite group of minerals forms a morphotropic series with the minerals olivine and brucite. The members of the humite group contain layers of the olivine structure that alternate with layers of the brucite-like sheets. The minerals are characterized by a complex set of bands in the 800 to 1000 cm-1 region attributed to the stretching vibrations of the olivine (SiO4)4- units.  The number of bands in this region is influenced by the number of olivine layers. Characteristic bending modes of the (SiO4)4- units are observed in the 500 to 650 cm-1 region. The brucite sheets are characterized by the OH stretching vibrations in the 3475 to 3625 cm-1.  The position of the OH stretching vibrations is determined by the strength of the hydrogen bond formed between the brucite-like OH units and the olivine silica layer. The number of olivine sheets and not the chemical composition determines the strength of the hydrogen bonds
Raman spectroscopy of uranopilite of different origin\ud
- implications for molecular structure

Uranopilite, \[(UO2)6(SO4)O2(OH)6(H2O)6](H2O)8, the composition of which may vary, can be understood as a complex hydrated uranyl oxy hydroxy sulfate. The structure of uranopilite of different localities has been studied by Raman spectroscopy at 298 and 77 K.  A single intense band at 1009 cm-1 assigned to the ￮1 (SO4)2- symmetric stretching mode shifts to higher wavenumbers at 77 K.  Three low intensity bands are observed at 1143, 1117 and 1097 cm-1. These bands are attributed to the (SO4)2- ν3 antisymmetric stretching modes.  Multiple bands provide evidence that the symmetry of the sulphate anion in the uranopilite structure is lowered. Three bands are observed at 843 to 816 cm-1 in both 298 and 77 K spectra and are attributed to the ν1 symmetric stretching modes of the (UO2)2+ units. Multiple bands prove the symmetry reduction of the UO2 ion. Multiple OH stretching modes prove a complex arrangement of OH groupings and hydrogen bonding in the crystal structure.  A series of infrared bands not observed in the Raman spectra are found at 1559, 1540, 1526 and 1511 cm-1 attributed to ￤ UOH bending modes. U-O bond lengths in uranyl and O-H…O bond lengths are calculated and compared with X-ray single crystal structure analysis. Raman spectra of uranopilites of different origin show subtle differences in spectra proving the spectra are origin and sample dependent. Hydrogen-bonding network and its arrangement in the crystal structure play an important role in the origin and stability of uranopilite