scholarly journals X-ray Structure Refinement and Vibrational Spectroscopy of Metavauxite FeAl2(PO4)2(OH)2·8H2O

Crystals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 297
Author(s):  
Giancarlo Della Ventura ◽  
Francesco Capitelli ◽  
Giancarlo Capitani ◽  
Gennaro Ventruti ◽  
Alessandro Monno
Keyword(s):  
Hydrogen Bonding ◽  
Structure Refinement ◽  
Methodological Approach ◽  
Broad Band ◽  
Frequency Region ◽  
Hydroxyl Group ◽  
Octahedral Complex ◽  
Hydrogen Atoms ◽  
High Frequency Region ◽  
X Ray

In this paper, we provide a crystal-chemical investigation of metavauxite, ideally FeAl2(PO4)2(OH)2·8H2O, from Llallagua (Bolivia) by using a multi-methodological approach based on EDS microchemical analysis, single crystal X-ray diffraction, and Raman and Fourier transform infrared (FTIR) spectroscopy. Our new diffraction results allowed us to locate all hydrogen atoms from the structure refinements in the monoclinic P21/c space group. Metavauxite structure displays a complex framework consisting of a stacking of [Al(PO4)3(OH)(H2O)2]7− layers linked to isolated [Fe(H2O)6]2+ cationic octahedral complex solely by hydrogen bonding. The hydrogen-bonding scheme was inferred from bond-valence calculations and donor-acceptor distances. Accordingly, strong hydrogen bonds, due to four coordinated H2O molecules, bridge the [Fe(H2O)6]2+ units to the Al/P octahedral/tetrahedral layer. The hydroxyl group, coordinated by two Al atoms, contributes to the intra-layer linkage. FTIR and Raman spectra in the high-frequency region (3700–3200 cm−1) are very similar, and show a complex broad band consisting of several overlapping components due to the H2O molecules connecting the isolated Fe(H2O)6 and the adjacent Al/P octahedral/tetrahedral layers. A sharp peak at 3540 cm−1 is assigned to the stretching mode of the OH group. The patterns collected in the low-frequency region are dominated by the stretching and bending modes of the PO43− group and the metal-oxygen polyhedra.

Structure, Stereochemistry and Novel 'Hydrogen Bonding' in Two Bipyridinium Salts of the B10H102- Anion

1987 ◽  
Vol 40 (12) ◽  
pp. 2097 ◽  
Author(s):  
DJ Fuller ◽  
DL Kepert ◽  
BW Skelton ◽  
AH White
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Charge Transfer ◽  
Single Crystal ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
Structure Determinations ◽  
Positively Charged

Crystal structure determinations of (LH)2(B10H10), (1), and (LH2)(B10H10), (2), L = 2,2'- bipyridine , have been carried out by single-crystal X-ray diffraction methods at 295 K, being refined by full-matrix least squares to residuals of 0.041, 0.047 for 1758, 1771 'observed' independent reflections respectively. Crystals of (1) are monoclinic, P21/n, a 12.040(7), b 17.71(1), c 11.142(4) �, β 101.78(4)�, Z 4. Crystals of (2) are monoclinic, P21/c, a 9.937(4), b 10.837(3), c 14.856(5) �, β 109 2l(3)�, Z 4. The colour of the compounds is accounted for by charge-transfer interactions of a novel type, namely between the positively charged cationic acid hydrogen atoms and the negatively charged non-apical hydrogen atoms of the anion. In yellow (1), these distances are 2.26(5) �, while in red (2), they are much shorter, being 1.89(4), 1.97(3) �.

A simple approach to estimate isotropic displacement parameters for hydrogen atoms

2015 ◽  
Vol 71 (2) ◽  
pp. 169-174 ◽  
Author(s):  
Anders Østergaard Madsen ◽  
Anna Agnieszka Hoser
Keyword(s):  
Structure Refinement ◽  
Simple Approach ◽  
Large Temperature ◽  
Neutron Diffraction Data ◽  
Hydrogen Atoms ◽  
Temperature Dependent ◽  
X Ray ◽  
Common Structure ◽  
Additive Term ◽  
Simple Combination

A simple combination of riding motion and an additive term is sufficient to estimate the temperature-dependent isotropic displacement parameters of hydrogen atoms, for use in X-ray structure refinements. The approach is validated against neutron diffraction data, and gives reasonable estimates in a very large temperature range (10–300 K). The model can be readily implemented in common structure refinement programs without auxiliary software.

Conformation of the esters of steroid hydroxyl groups by infrared spectroscopy

1969 ◽  
Vol 47 (9) ◽  
pp. 1601-1603 ◽  
Author(s):  
C. R. Narayanan ◽  
M. R. Sarma ◽  
T. K. K. Srinivasan ◽  
M. S. Wadia
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectroscopy ◽  
Carbonyl Group ◽  
Hydroxyl Group ◽  
Spectral Studies ◽  
Hydroxyl Groups ◽  
Hydrogen Atoms ◽  
Infrared Spectral

Infrared spectral studies show that the carbonyl group of the esters of steroid hydroxyl groups are stabilized near the adjacent alkyl hydrogen atoms; this energy of stabilization appears to be more than that of hydrogen bonding between the carbonyl and a nearby hydroxyl group.

The Crystal and Molecular Structure of trans-Dichloro-mer-trans-bis (triisopropylphosphine)(phosphine)hydridoiridium(III)

1995 ◽  
Vol 48 (7) ◽  
pp. 1277 ◽  
Author(s):  
EJ Ditzel ◽  
GB Robertson
Keyword(s):  
Molecular Structure ◽  
Transition Metal ◽  
Crystal And Molecular Structure ◽  
Structure Refinement ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Full Matrix ◽  
X Ray ◽  
Molecular Dimensions

The structure of mer-trans-(PPri3)2(PH3)H-trans-Cl2IrIII (1) (Pri = isopropyl), the second third-row transition-metal-PH3 complex to be so characterized, has been determined by single-crystal X-ray diffraction analysis. Crystals are monoclinic, space group C 2/c with a 21.701(2), b 8.735(1), c 15.594(1) Ǻ, β 119.57(1)° and Z 4. Structure refinement by full-matrix least-squares analysis (2811 reflections, 113 parameters) converged with R = 0.016 and Rw = 0.022. Molecules exhibit crystallographically imposed C2 symmetry. The C2 axis passes through the iridium, hydride and PH3 phosphorus atoms, and requires the PH3 hydrogen atoms to be disordered. Important molecular dimensions are Ir-PPri3 2.371(1) Ǻ, Ir-PH3 2.362(1) Ǻ, Ir-Cl 2.374(1) Ǻ and P- Ir -P(trans) 163.21(3)°.

Lewis-Base Adducts of Lead(II) Compounds. X. Synthetic and Structural Studies of Some 1:1 Adducts of 'tet-b' With Lead(II) (Pseudo-)Halides

1996 ◽  
Vol 49 (10) ◽  
pp. 1067 ◽  
Author(s):  
JM Harrowfield ◽  
H Miyamae ◽  
BW Skelton ◽  
AA Soudi ◽  
AH White
Keyword(s):  
Hydrogen Bonding ◽  
Room Temperature ◽  
Lewis Base ◽  
Double Salt ◽  
Rear Side ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Hydrogen Bonding Interactions ◽  
Structure Determinations ◽  
Pseudo Halides

Syntheses and room-temperature single-crystal X-ray structure determinations are recorded for 1 : 1 adducts of (7R*,14R*)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane (' tet -b') with a variety of lead(II) salts. [( tet -b)PbCl2] is monoclinic, P 21/c, a 7.183(3), b 12.425(2), c 24.418(2) Ǻ, β 95.32(3)°, Z = 4; conventional R on |F| was 0.044 for 3188 independent, 'observed' (I > 3σ(I)) reflections. [( tet -b)PbI2] is monoclinic, P 21/c, a 19.920(5), b 7.772(5), c 15.605(6) Ǻ, β 108.39(2)°, Z = 4; R 0.051 for No 2507. [( tet -b) Pb (NCS)2] is orthorhombic, P 212121, a 36.99(1), b 8.996(5), c 6.964(3) Ǻ, Z = 4; R 0.043 for No 2100. All are discrete mononuclear [( tet -b)PbX2] entities in which the macrocyclic N4 ligand occupies one 'face' of the N4PbX2 coordination sphere, the thiocyanate ligands being N-bonded, with Pb -N-C angles of 116(2) and 118(1)°; interesting hydrogen-bonding interactions are found, columns of molecules being formed by way of hydrogen bonding between the coordinated (pseudo-)halides and the NH hydrogen atoms which project to the 'rear' face of the ligand of the next molecule, opposite the metal. In contrast to these, the bromide analogue, monoclinic, P21, a 9.342(3), b 12.720(5), c 18.845(5) Ǻ, β 103.17(2)°, Z = 4, R 0.035 for No 3593, is best formulated as [( tet -b) PbBr ] Br, one only of the bromide entities being bound to the lead, the other being fully dissociated by hydrogen bonding/ion pairing to the 'rear' side of adjacent ligands , forming hydrogen-bonded sheets rather than columns. This formulation has been extended to provide a description of an analogous mixed chloride- perchlorate 'double salt', [( tet -b) PbCl ] (ClO4).CH3OH, which is orthorhombic, P 212121, a 19.475(2), b 18.73(1), c 6.820(2) Ǻ, Z = 4, R 0.054 for No 3075. However, another double salt, modelled in refinement as Pb ( tet -b)Cl0.5(ClO4)1.5.H2O, orthorhombic Pnma , a 20.640(5), b 26.16(1), c 8.937(4) Ǻ, Z = 4 dimers , R 0.074 for No 1769, is in this case more appropriately described as [( tet -b) Pb (OClO2O)2Pb( tet -b)] (ClO4) Cl.H2O with perchlorate rather than halide coordinated, and an incipiently dimeric cation, as in the parent [( tet -b) Pb (OClO3)]2 (ClO4)2.2H2O.

scholarly journals Structural and vibrational spectroscopic studies of new phases with sillenite type in the system Bi2O3- In2O3 –MgO

2020 ◽  
Vol 10 (1) ◽  
pp. 90-98
Author(s):  
Hajar Ait Oulahyane ◽  
Abdeslam Chagraoui ◽  
Leila Loubbidi ◽  
Lamia Bourja ◽  
Omar Ait Sidi Ahmed ◽  
...  
Keyword(s):  
High Frequency ◽  
Lone Pair ◽  
Rietveld Analysis ◽  
Spectroscopic Studies ◽  
Frequency Region ◽  
Family Type ◽  
X Ray Diffraction ◽  
High Frequency Region ◽  
X Ray ◽  
Full Profile

The anion and cation deficient phase Bi0.95 In0.05 O1.5 (Bi1.9 In0.1 O3) was synthesized and experimentally investigated using X-ray diffraction and vibrational spectroscopy (Infrared and Raman). The non-stoichiometric phases are similar to sillenite family type γBi2O3 and crystallize in the I23 space group. The crystal structure was determined by full profile Rietveld analysis of the powder diffractogram. It is formed by a sequence of BiO5E polyhedra (E lone pair of bismuth) and MO4 polyhedra (M = In, Mg). The set of MO4 polyhedra are localized in cavities generated by BiO5E polyhedra. The vibrational spectroscopic study revealed the existence of three regions; low, intermediate and high-frequency region. They are attributed to Bi-O stretching mode, In / Mg-O vibrations and cationic displacements respectively.

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

2020 ◽  
Vol 76 (3) ◽  
pp. 296-306 ◽  
Author(s):  
Kunal Kumar Jha ◽  
Barbara Gruza ◽  
Prashant Kumar ◽  
Michal Leszek Chodkiewicz ◽  
Paulina Maria Dominiak
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Bond Lengths ◽  
Atom Model ◽  
User Friendly

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

scholarly journals Temperature dependence of Uiso constraints in riding hydrogen treatments

2014 ◽  
Vol 70 (a1) ◽  
pp. C286-C286
Author(s):  
Jens Luebben ◽  
Simon Grabowsky ◽  
Alison Edwards ◽  
Wolfgang Morgenroth ◽  
George Sheldrick ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structure Refinement ◽  
Heavy Atom ◽  
Data Sets ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Structure Determinations ◽  
Thermal Displacements ◽  
Conventional Structure ◽  
Oniom Approach

"Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."

scholarly journals Anomalous Amide Proton Chemical Shifts as Signatures of Hydrogen Bonding to Aromatic Sidechains

2021 ◽  
Author(s):  
Kumaran Baskaran ◽  
Colin W. Wilburn ◽  
Jonathan R. Wedell ◽  
Leonardus M. I. Koharudin ◽  
Eldon L. Ulrich ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Aromatic Ring ◽  
Structure Refinement ◽  
Protein Structures ◽  
Amide Proton ◽  
Hydrogen Atoms ◽  
Local Accuracy ◽  
Amide Protons

Abstract. Hydrogen bonding between an amide group and the p-π cloud of an aromatic ring was first identified in a protein in the 1980s. Subsequent surveys of high-resolution X-ray crystal structures found multiple instances, but their preponderance was determined to be infrequent. Hydrogen atoms participating in a hydrogen bond to the p-π cloud of an aromatic ring are expected to experience an upfield chemical shift arising from a shielding ring current shift. We survey the Biological Magnetic Resonance Data Bank for amide hydrogens exhibiting unusual shifts as well as corroborating nuclear Overhauser effects between the amide protons and ring protons. We find evidence that Trp residues are more likely to be involved in p-π hydrogen bonds than other aromatic amino acids, whereas His residues are more likely to be involved in hydrogen bonds with a ring nitrogen acting as the hydrogen acceptor. The p-π hydrogen bonds may be more abundant than previously believed. The inclusion in NMR structure refinement protocols of shift effects in amide protons from aromatic side chains, or explicit hydrogen bond restraints between amides and aromatic rings, could improve the local accuracy of side-chain orientations in solution NMR protein structures, but their impact on global accuracy is likely be limited.

scholarly journals The crystal structure of Cs2S2O3·H2O

2016 ◽  
Vol 71 (5) ◽  
pp. 579-584 ◽  
Author(s):  
Verena Winkler ◽  
Marc Schlosser ◽  
Arno Pfitzner
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Ir Spectroscopy ◽  
Alkali Metal ◽  
Title Compound ◽  
Structure Refinement ◽  
Free Water ◽  
Hydrogen Atoms ◽  
Bending Modes ◽  
Unit Cell Dimensions

AbstractA reinvestigation of the alkali metal thiosulfates has led to the new phase Cs2S2O3·H2O. At first cesium thiosulfate monohydrate was obtained as a byproduct of the synthesis of Cs4In2S5. Further investigations were carried out using the traditional synthesis reported by J. Meyer and H. Eggeling. Cs2S2O3·H2O crystallizes in transparent, colorless needles. The crystal structure of the title compound was determined by single crystal X-ray diffraction at room temperature: space group C2/m (No. 12), unit cell dimensions: a = 11.229(4), b = 5.851(2), c = 11.260(5) Å, β = 95.89(2)°, with Z = 4 and a cell volume of V = 735.9(5) Å3. The positions of all atoms including the hydrogen atoms were located in the structure refinement. Cs2S2O3·H2O is isotypic with Rb2S2O3·H2O. Isolated tetrahedra [S2O3]2− are coordinated by the alkali metal cations, and in addition they serve as acceptors for hydrogen bonding. For both Cs atoms the shortest distances are observed to oxygen atoms of the S2O32− anions whereas the terminating sulfur atom has its shortest contacts to the water hydrogen atoms. Thus, an extended hydrogen bonding network is formed. The title compound has also been characterized by IR spectroscopy. IR spectroscopy reveals the vibrational bands of the water molecules at 3385 cm−1. They show a red shift in the OH stretching and bending modes as compared to free water. This is due both to the S···H hydrogen bonding and to the coordination of H2O molecules to the cesium atoms.

Sign in / Sign up

Export Citation Format

Share Document