H-bonding Scheme Research Articles

On the crystal-chemistry of meyerhofferite, CaB3O3(OH)5·H2O

The crystal structure and crystal chemistry of meyerhofferite, ideally CaB3O3(OH)5·H2O, was investigated by a multi-methodological approach based on titrimetric determination of boron, gravimetric determination of calcium, determination of fluorine by ion selective electrode, determination of water content by heating, other minor elements by inductively coupled plasma atomic emission spectroscopy, along with single-crystal synchrotron X-ray and neutron diffraction. The concentration of more than 50 chemical elements was measured. The combination of these techniques proves that the composition of meyerhofferite approaches the ideal one (i.e., (Ca1.012Mg0.003) (B2.984Si0.001)O3(OH)5·1.018H2O), with only a modest fraction of Mg (with MgO ≈ 0.03 wt%) replacing Ca, and with Si the only potential substituent of tetrahedral B (with SiO2 ≈ 0.02 wt%). The content of REE and other minor elements is, overall, not significant, including that of fluorine as a potential OH− substituent (i.e., < 0.01 wt%). These findings have some relevant geochemical and technical implications, here discussed. The X-ray and neutron structure model obtained in this study prove that the building units of the structure of meyerhofferite consist of: two BO2(OH)2 tetrahedra and one BO2(OH) triangle, linked by corner-sharing to form [B3O3(OH)5]2− rings, and distorted Ca-polyhedra (with CN = 8, CaO3(OH)4(OH2)), linked by edge-sharing to form infinite chains along [001]. The B3O3(OH)5 rings are connected to the Ca-polyhedra chains by corner- and edge-sharing, on two sides of the chains. These heteropolyhedral chains, made by Ca-polyhedra and B3O3(OH)5 rings, are mutually connected through hydrogen bonding only, giving rise to the tri-dimensional edifice of meyerhofferite. The neutron structure refinement showed no evidence of static or dynamic disorder pertaining to the H sites; their libration regime was found to be significantly anisotropic. At least seven of the nine oxygen sites of the structure are involved in H-bonding, as donors or as acceptors. The role played by the H-bonding scheme on the physical properties of meyerhofferite is discussed.

Studies on the Vitrified and Cryomilled Bosentan.

In this paper, several experimental techniques [X-ray diffraction, differential scanning calorimetry (DSC), thermogravimetry, Fourier transform infrared spectroscopy, and broad-band dielectric spectroscopy] have been applied to characterize the structural and thermal properties, H-bonding pattern, and molecular dynamics of amorphous bosentan (BOS) obtained by vitrification and cryomilling of the monohydrate crystalline form of this drug. Samples prepared by these two methods were found to be similar with regard to their internal structure, H-bonding scheme, and structural (α) dynamics in the supercooled liquid state. However, based on the analysis of α-relaxation times (dielectric measurements) predicted for temperatures below the glass-transition temperature (Tg), as well as DSC thermograms, it was concluded that the cryoground sample is more aged (and probably more physically stable) compared to the vitrified one. Interestingly, such differences in physical properties turned out to be reflected in the lower intrinsic dissolution rate of BOS obtained by cryomilling (in the first 15 min of dissolution test) in comparison to the vitrified drug. Furthermore, we showed that cryogrinding of the crystalline BOS monohydrate leads to the formation of a nearly anhydrous amorphous sample. This finding, different from that reported by Megarry et al. [Carbohydr. Res.2011, 346, 1061−106421492830] for trehalose (TRE), was revealed on the basis of infrared and thermal measurements. Finally, two various hypotheses explaining water removal upon cryomilling have been discussed in the manuscript.

H-bonding in lazulite: a single-crystal neutron diffraction study at 298 and 3 K

The crystal structure and crystal chemistry of a lazulite from Crosscut Creek (Kulan Camp area, Dawson mining district, Yukon, Canada) was investigated by electron microprobe analysis in wavelength-dispersive mode (EMPA) and single-crystal neutron diffraction at 298 and 3 K. Its empirical formula, based on EMPA data, is: (Mg0.871Fe0.127)Σ0.998Al2.030(P1.985Ti0.008Si0.007O4)2(OH)2. The neutron diffraction experiments at room and low T proved that the H-free structural model of lazulite previously reported, on the basis of X-ray structure refinement, is correct: the building unit of the lazulite structure consists of a group of three face-sharing (Al-octahedron) + (Mg,Fe-octahedron) + (Al-octahedron), connected to the adjacent one via a corner-shared OH-group and two corner-shared oxygen sites of the P-tetrahedron, to form a dense 3D-edifice. Only one crystallographically independent H site occurs in the structure of lazulite, forming a hydroxyl group with the O5 oxygen, with O5–H = 0.9997 A at room temperature (corrected for riding motion effect). The H-bonding scheme in the structure of lazulite is now well defined: a bifurcated bonding scheme occurs with the O4 and O2 oxygen sites as acceptors. The two H-bonds are energetically different, as shown by their bonding geometry: the H-bond with the O2 site as acceptor is energetically more favorable, being O5–H···O2 = 152.67(9)°, O5···O2 = 3.014(1) A and H···O2 = 2.114(1) A, whereas that with O4 as acceptor is energetically more costly, being O5–H···O4 = 135.73(8)°, O5···O4 = 3.156(1) A and H···O4 = 2.383(1) A, at room temperature. No T-induced phase transition occurs within the T-range investigated. At low temperature, the O5–H···O2 bond is virtually identical to the room-T one, whereas the effects of T on O5–H···O4 are more pronounced, with significant differences of the Odonor···Oacceptor and H···Oacceptor distances. The experimental findings of this study do not support the occurrence of HPO4 or H2PO4 units into the structure of lazulite, recently reported on the basis of infrared and Raman spectra.

Hydroxylgugiaite: A New Beryllium Silicate Mineral From the Larvik Plutonic Complex, Southern Norway and the Ilímaussaq Alkaline Complex, South Greenland; The First Member of the Melilite Group To Incorporate A Hydrogen Atom

Abstract Hydroxylgugiaite, ideally (Ca 3 □ 1 ) Σ4 (Si 3.5 Be 2.5 ) Σ6 O 11 (OH) 3 , is a new mineral species from two localities in the Larvik plutonic complex in Porsgrunn, Telemark, Norway, and one locality in Ilimaussaq, Greenland. Hydroxylgugiaite crystals occur as squat dipyramids {111} (30 × 50 μm) or as elongate tetragonal prisms. The crystals are translucent, white to pale grey in color, with a white streak and vitreous luster. It is brittle, with no apparent cleavage. Hydroxylgugiaite is uniaxial positive with ω = 1.622 ± 0.002 and ϵ = 1.632 ± 0.002. There is no pleochroism and birefringence is low. The average of eight analyses of a single grain of type material (oxide wt.%) gave Na 2 O 2.04, CaO 32.90, FeO 0.22, MnO 0.74, BeO 13.47 (LA-ICP-MS), Al 2 O 3 0.74, SiO 2 44.06, F 1.74, H 2 O (assuming 3 OH + F) 4.93, Total (–0.73 O = F) 100.10. Potassium, strontium, and magnesium were measured but not detected. The calculated density is 2.79 g cm –3 . The empirical formula on the basis of 14 anions including 3 OH – + F – is: (Ca 2.76 Na 0.31 Mn 0.05 Fe 0.01 ) Σ3.13 (Si 3.45 Be 2.53 Al 0.07 ) Σ6.05 O 11 [(OH) 2.57 F 0.43 ] Σ3 . The formula from crystal-structure analysis of the Saga specimen is: (Ca 3.02 □ 0.98 ) Σ4 (Si 1.79 Be 0.21 ) Σ2 (Be 2.29 Si 1.71 ) Σ4 O 11 (OH) 3 . Combined structural and chemical data gives the following formula for the Nakkaalaaq specimen: (Ca 2.88 □ 0.98 Na 0.12 Mn 0.02 ) Σ4 (Si 1.80 Be 0.17 Al 0.03 ) Σ2 (Be 2.32 Si 1.68 ) Σ4 O 11 [(OH) 2.70 F 0.30 ] Σ3 ; with simplified formula (Ca,□) 4 (Si,Be) 2 (Be,Si) 4 O 11 (OH) 3 . The crystal structure of hydroxylgugiaite is tetragonal in acentric space group P 2 1 / m , with a 7.4151(2), b 7.4151, c 4.9652(1) A, V 272.9(1) A 3 , and Z = 1. It has been refined to an R index of 0.028 on the basis of 342 observed reflections and a correction for the {110} twin law. It is an H-bearing member of the melilite group. The structure has two distinct layers. The one crystallographically distinct Ca site with eight-fold coordination is a square antiprism polyhedron. The Ca polyhedra are in a layer with the H atoms. A second layer consists of corner-sharing Si/Be atoms in tetrahedral coordination with O. One H atom is bonded to an apical O atom that is not shared by two tetrahedra. This H atom is present only when there is a Ca -site vacancy. The other H atom is loosely bonded to the same O atom but at a different site. The IR spectrum supports this H-bonding scheme. Additional hydroxylgugiaite data is given for the other localities.

H-bonding scheme in allactite: a combined single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, FTIR and EPMA-WDS study

AbsatractThe crystal chemistry of allactite from Långban, Värmland (Sweden) was investigated by single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, Fourier-transform infra-red spectroscopy (FTIR) and electron microprobe analysis by wavelength-dispersive spectroscopy (EPMA-WDS). The optical spectra indicate the presence of Mn in valence state 2+ only. Assuming 16 O atoms per formula unit, arsenic as As5+ and the (OH) content calculated by charge balance, the resulting formula based on the EPMA-WDS data is (Mn2+6.73Ca0.13Mg0.12Zn0.02)∑7.00(As5+)2.00O16H8, very close to the ideal composition Mn7(AsO4)2(OH)8. In the unpolarized FTIR spectrum of allactite, fundamental (OH)-stretching bands are observed at 3236, 3288, 3387, 3446, 3484, 3562 and 3570 cm–1, suggesting that a number of OH environments, with different hydrogen bond strengths, occur in the structure. The neutron structure refinement shows that four independent H sites occur in allactite with full site occupancy, all as members of hydroxyl groups. The complex hydrogen-bonding scheme in the allactite structure is now well defined, with at least nine hydrogen bonds energetically favourable with mono-, bi- and trifurcated configurations.

H-bonding scheme and cation partitioning in axinite: a single-crystal neutron diffraction and Mössbauer spectroscopic study

The crystal chemistry of a ferroaxinite from Colebrook Hill, Rosebery district, Tasmania, Australia, was investigated by electron microprobe analysis in wavelength-dispersive mode, inductively coupled plasma–atomic emission spectroscopy (ICP–AES), 57Fe Mossbauer spectroscopy and single-crystal neutron diffraction at 293 K. The chemical formula obtained on the basis of the ICP–AES data is the following: $$ ^{X1,X2} {\text{Ca}}_{4.03} \,^{Y} \left( {{\text{Mn}}_{0.42} {\text{Mg}}_{0.23} {\text{Fe}}^{2 + }_{1.39} } \right)_{\varSigma 2.04} \,^{Z1,Z2} \left( {{\text{Fe}}^{3 + }_{0.15} {\text{Al}}_{3.55} {\text{Ti}}_{0.12} } \right)_{\varSigma 3.82} \,^{T1,T2,T3,T4} \left( {{\text{Ti}}_{0.03} {\text{Si}}_{7.97} } \right)_{\varSigma 8} \,^{T5} {\text{B}}_{1.96} {\text{O}}_{30} \left( {\text{OH}} \right)_{2.18} $$ . The 57Fe Mossbauer spectrum shows unambiguously the occurrence of Fe2+ and Fe3+ in octahedral coordination only, with Fe2+/Fe3+ = 9:1. The neutron structure refinement provides a structure model in general agreement with the previous experimental findings: the tetrahedral T1, T2, T3 and T4 sites are fully occupied by Si, whereas the T5 site is fully occupied by B, with no evidence of Si at the T5, or Al or Fe3+ at the T1–T5 sites. The structural and chemical data of this study suggest that the amount of B in ferroaxinite is that expected from the ideal stoichiometry: 2 a.p.f.u. (for 32 O). The atomic distribution among the X1, X2, Y, Z1 and Z2 sites obtained by neutron structure refinement is in good agreement with that based on the ICP–AES data. For the first time, an unambiguous localization of the H site is obtained, which forms a hydroxyl group with the oxygen atom at the O16 site as donor. The H-bonding scheme in axinite structure is now fully described: the O16–H distance (corrected for riding motion effect) is 0.991(1) A and an asymmetric bifurcated bonding configuration occurs, with O5 and O13 as acceptors [i.e. with O16···O5 = 3.096(1) A, H···O5 = 2.450(1) A and O16–H···O5 = 123.9(1)°; O16···O13 = 2.777(1) A, H···O13 = 1.914(1) A and O16–H···O13 = 146.9(1)°].

On the complex H-bonding network in paravauxite, Fe2+Al2(PO4)2(OH)2·8H2O: A single-crystal neutron diffraction study

AbstractThe crystal structure and the chemical composition of a paravauxite from the Siglo Veinte Mine, Llallagua, Bustillo Province, Potosi Department, Bolivia [Fe(Fe0.9162+Mn0.0162+Mg0.064Ca0.002)∑0.998Al(1)Al(2)Al2.005P(P1.998Si0.002)∑2O8(OH)2·8H2O, a = 5.242(1) Å, b = 10.569(2) Å, c = 6.970(2) Å, α = 106.78(3)°, β = 110.81(2)° and γ = 72.29(2)°, space group P], was investigated by single-crystal neutron diffraction and electron microprobe analysis in wavelength-dispersive mode. Neutron-intensity data were collected at 293 K and anisotropic structure refinement was performed. At the end of the refinement no peak larger than ±1.3 fm/Å3 was present in the final difference-Fourier map of the nuclear density. The final statistical index was R1 = 0.0495 for 194 refined parameters and 1678 unique reflections with Fo &gt; 4σ(Fo). Eleven independent H sites (i.e. H(1), H(2), H(3), H(4A), H(4B), H(5), H(6), H(7), H(8), H(9A) and H(9B)), all at ∼1 Å from the respective O sites, were located successfully. H(4A) and H(4B) and H(9A) and H(9B) are two mutually exclusive subsite couples only 0.4−0.6 Å apart. The complex H-bonding scheme in the paravauxite structure is now well defined and 12 independent H bonds, with an energetically favourable bonding configuration, are described. A comparison between the previous experimental findings based on Raman and infrared spectroscopy and those obtained in this present study is carried out. Paravauxite provides the rare opportunity to investigate the H-bond configuration of coexisting hydroxyl groups and H2O molecules in minerals by single-crystal neutron diffraction. H2O is present as zeolitic (i.e. lying in the cavities) and non-zeolitic H2O (i.e. bonded to Al or Fe to form Al or Fe octahedra).

Aripiprazole salts IV. Anionic plus solvato networks defining molecular conformation

Five new examples of aripiprazole (arip) salts are presented, viz., the Harip phthalate [Harip+·C8H5O4−(I)], homophthalate [Harip+·C9H7O4−(II)] and thiosalicilate [Harip+·C7H4O2S−(III)] salts on one side, and two different dihidrogenphosphates, Harip+·H2PO4−·2(H3PO4)·H2O (IV) and Harip+·H2PO4−·H3PO4(V). Regarding the internal structure of the aripH+ cations, they do not differ from the already known moieties in bond distances and angles, while interesting differences in conformation can be observed, setting them apart in two groups: those in I, II and III present similar conformations to those in the so far reported arip salts presenting the same centrosymmetric R(8)22 dimeric synthon, but different to those in IV and V. In parallel, the anion (+ acid) groups define bulky systems of different dimensionality (1D in the former group, 2D in the latter). The correlation between arip molecular conformation and anionic network type is discussed. An interesting feature arises with the water solvato molecule in IV, disordered around an inversion center, in regard with its interaction with an (also disordered) phosphato O–H, in a way that an “orderly disordered” H-bonding scheme arises, complying with the S.G. symmetry requirements only on average.

A low temperature X-ray single-crystal diffraction and polarised infra-red study of epidote

The effects of low-temperature on the crystal structure of a natural epidote [Ca1.925Fe0.745Al2.265Ti0.004Si3.037O12(OH), a = 8.8924(7), b = 5.6214(3), c = 10.1547(6)A and β = 115.396(8)° at room conditions, Sp. Gr. P21 /m] have been investigated with a series of structure refinements down to 100 K on the basis of X-ray single-crystal diffraction data. The reflection conditions confirm that the space group is maintained within the T-range investigated. Structural refinements at all temperatures show the presence of Fe3+ at the octahedral M(3) site only [%Fe(M3) = 70.6(4)% at 295 K]. Only one independent proton site was located and two possible H-bonds occur, with O(10) as donor and O(4) and O(2) as acceptors. The H-bonding scheme is maintained down to 100 K and is supported by single crystal room-T polarised FTIR data. FTIR Spectra over the region 4,000–2,500 cm−1 are dominated by the presence of a strongly pleochroic absorption feature which can be assigned to protonation of O(10)–O(4). Previously unobserved splitting of this absorption features is consistent with a NNN influence due to the presence of Al and Fe3+ on the nearby M(3) site. An additional relatively minor absorption feature in FTIR spectra can be tentatively assigned to protonation of O(10)–O(2). Low-T does not affect significantly the tetrahedral and octahedral bond distances and angles, even when distances are corrected for “rigid body motions”. A more significant effect is observed for the bond distances of the distorted Ca(1)- and Ca(2)-polyhedra, especially when corrected for “non-correlated motion”. The main low-T effect is observed on the vibrational regime of the atomic sites, and in particular for the two Ca-sites. A significant reduction of the magnitude of the thermal displacement ellipsoids, with a variation of U eq (defined as one-third of the trace of the orthogonalised U ij tensor) by ~40% is observed for the Ca-sites between 295 and 100 K. Within the same T-range, the U eq of the octahedral and oxygen sites decrease similarly by ~35%, whereas those of the tetrahedral cations by ~22%.

Hydrogen-bond and cation partitioning in muscovite: A single-crystal neutron-diffraction study at 295 and 20 K

The crystal chemistry of a pegmatitic Fe-bearing muscovite (with FeO ~5.1 wt%) from Val di Crana, Arvogno (Verbania, Nothern Italy) has been investigated by means of wavelength-dispersive X-ray spectroscopy and constant-wavelength [λ = 0.9462(2) Å] single-crystal neutron diffraction at 295 and 20 K (2θmax = 90°). The structure refinement at 295 K shows no significant deviation from the full occupancy of the K site (using the scattering length of potassium alone), and a disordered Si/Aldistribution in the two independent tetrahedral sites (i.e., T1 and T2) and Fe/Al-distribution in the M2 octahedral site. The difference Fourier map of the nuclear density shows that only one independent H site occurs in the muscovite structure, at both room and low temperature. No evidence of disorder in two sub-sites, as observed in a previous study, was found. The thermal displacement of the H site is here described anisotropically. A trifurcated hydrogen bonding scheme was found: the O6-H bond distance corrected for “riding motion” is ~0.984 Å at 295 K, and three significantly weak hydrogen bonds to the O atoms O2, O4, and O6 occur, with H···O2 = 2.635(5), H···O4 = 2.657(4), and H···O5 = 2.647(4) Å and O6-H···O angles all similar in value (~138°). The structure refinements show that the structure configuration of muscovite is maintained at least down to 20 K: the cation disordering in the tetrahedral and octahedral site and the H-bonding scheme are preserved. The structural evolution induced by decreasing temperature is governed by the contraction along a direction perpendicular to (001), mainly due to the compression of the “inner” K-O bonds, which leads to an increase of the tetrahedral rotation angle (α) of the six-membered ring. A further effect in response to lowering the temperature is a significant reduction of the magnitude of the thermal displacement parameters.

G^C Quartet — A DNA-Inspired Janus-GC Heterocycle: Synthesis, Structural Analysis, and Self-Organization

In this communication we disclose the synthesis and characterization of a DNA-inspired self-complementary heterocycle that contains AAD-DAA H-bond acceptor/donor patterns. Whereas in the past such AAD-DAA self-complementarity has given rise to trimeric and hexameric rosettes, we now demonstrate that the same H-bonding scheme, when properly arrayed, can be used to program a tetrameric rosette, which unlike a G-quartet requires no metal binding or peripheral components for preorganization. Of note, we exploit both 2D-NOESY and DOSY 1H NMR to substantiate the tetrameric stoichiometry in this noncovalent rosette comprising 12 H-bonds.

Jahnsite-(NaFeMg), a new mineral from the Tip Top mine, Custer County, South Dakota: Description and crystal structure

Jahnsite-(NaFeMg), NaFe 3+ Mg 2 Fe 2 3+ (PO 4 ) 4 (OH) 2 ·8H 2 O, space group P 2/ a , a = 15.0811(16), b = 7.1403(8), c = 9.8299(11) A, β = 110.445(1)°, V = 991.8(2) A 3 , and Z = 2, is a new mineral from the Tip Top mine, Custer County, South Dakota. It occurs as the dominant chemical zone in transparent pseudo-orthorhombic twinned prisms up to 1 mm long with shallow wedge-like terminations, both as isolated twinned crystals and in subparallel to divergent intergrowths. The crystals are yellow with orange-red bands just below the terminations. The mineral has a white streak, vitreous luster, Mohs hardness of 4, and good {001} cleavage. The measured density is 2.58(2) g/cm 3 , and the calculated density is 2.608 g/cm 3 . It is optically biaxial (–), with α = 1.632(1), β = 1.669(1), γ = 1.671(1) (589 nm); 2 V (meas.) = 25(5)°, 2 V (calc.) = 26°; dispersion: r > v , very strong; orientation: Y = b , Z ^ a = +28° (in β obtuse); pleochroism: X = colorless, Y and Z = beige; Y = Z > X . Electron microprobe analyses provided: Na 2 O 2.82, CaO 0.34, MnO 0.32, MgO 10.27, Fe 2 O 3 27.35, P 2 O 5 35.93, H 2 O 21.58 (calc.), total 98.61, which in terms of the general formula for the whiteite-jahnsite group XM1M2 2 M3 2 (PO 4 ) 4 (OH) 2 ·8H 2 O, yields the empirical formula: (Na 0.72 Ca 0.05 Mn 0.04 2+ )(Fe 0.72 3+ Mg 0.01 )Mg 2.00 Fe 2.00 3+ (PO 3.77 OH 0.23 ) 4 (OH) 2 ·8H 2 O. Crystal structure refinement ( R 1 = 0.041) supports these cation site assignments. Typical crystals have as many as five chemical zones from base to termination corresponding to the following jahnsite species: jahnsite-(NaMnMg), jahnsite-(NaFeMg), jahnsite-(CaMnMg), jahnsite-(NaFeMg), jahnsite-(CaMgMg). The characterization of the new mineral jahnsite-(NaFeMg) is based upon the second zone listed, which corresponds to roughly 80% of the crystal volume. Jahnsite-(NaMnMg) and jahnsite-(CaMgMg) also represent new species; however, the very small volume of these zones is insufficient to permit complete characterization of these species. Jahnsite-(NaFeMg) is the first member of the whiteite-jahnsite group in which a monovalent cation (Na + ) predominantly occupies the X site and a trivalent cation (Fe 3+ ) the M1 site. The structure differs from that determined for jahnsite-(CaMnMg) in that the X site is [8]-coordinated and the M1 and P1 polyhedra exhibit greater distortions caused by cation-cation repulsion across their shared edges. The determination of H positions allows the elucidation of a definitive H-bonding scheme.

Propensity for local folding induced by the urea fragment in short-chain oligomers

Examination of local folding and H-bonding patterns in model compounds can be extremely informative to gain insight into the propensity of longer-chain oligomers to adopt specific folding patterns (i.e. foldamers) based on remote interactions. Using a combination of experimental techniques (i.e. X-ray diffraction, FT-IR absorption and NMR spectroscopy) and theoretical calculations at the density functional theory (DFT) level, we have examined the local folding patterns induced by the urea fragment in short-chain aza analogues of beta- and gamma-amino acid derivatives. We found that the urea-turn, a robust C(8) conformation based on 1<--3 H-bond interaction, is largely populated in model ureidopeptides (I-IV) obtained by replacing the alpha-carbon of a beta-amino acid by a nitrogen. This H-bonding scheme is likely to compete with remote H-bond interactions, thus preventing the formation of secondary structures based on remote intrastrand interactions in longer oligomers. In related oligomers obtained by the addition of a methylene in the main chain (V-VIII), nearest-neighbour H-bonded interactions are unfavourable i.e. the corresponding C9 folding pattern is hardly populated. In this series, folding based on remote intrastrand interactions becomes possible for longer oligomers. We present spectroscopic evidence that tetraurea VIII is likely to be the smallest unit capable of reproducing the H-bonded motif found in 2.5-helical N,N'-linked oligoureas.

THE ATOMIC STRUCTURE AND HYDROGEN BONDING OF DEUTERATED MELANTERITE, FeSO4{middle dot}7D2O

The atomic structure of synthetic, deuterated melanterite (FeSO4·7D2O), a 14.0774(9), b 6.5039(4), c 11.0506(7) A, β 105.604(1)°, space group P 21/ c , Z = 4, has been refined from the combined refinement of 2.3731(1) A and 1.3308 A neutron powder-diffraction data to a R wp (tot) = 3.01% and R p (tot) = 2.18%. Both the short- and long-wavelength data were required to obtain a satisfactory fit in the Rietveld refinement. The results of this study confirm the previously proposed H-bonding scheme for melanterite. Small but significant variations of the Fe–O bond lengths are attributed to details of the hydrogen bonds to the oxygen atoms of the Fe octahedra. We draw comparisons between the monoclinic and orthorhombic heptahydrate sulfate minerals associated with mine wastes and relate differences in the structure to strengths and weaknesses in their H-bond networks.

Thiamin Deprotonation Mechanism. Carbanion Development Stabilized by the LUMOs of Thiazolium and Pyrimidylimine Working in Tandem and Release Governed by a H-Bond Switch

Our previous paper (J. Phys. Chem. A 2005, 109, 7606) using computed atomic charges, based on the quantum theory of atoms in molecules (QTAIM), on azolium models of thiamin diphosphate has shown that only sulfur acts as an effective electron sink in the formation of the thiamin carbanion intermediate. Herein we apply natural bond orbital (NBO) theory to the analysis of orbital contributions to canonical molecular orbitals (CMOs) of six abbreviated azolium analogs of the carbanion to better understand the unique function of sulfur. The NBO/CMO data provide a description of the origin of the first thiamin electron sink: sulfur performing in the sigma- and pi-orbitals of the transition state as well as in the carbanion, and its advantages due to low electronegativity and moderate size. At the next level of thiamin modeling, we include the six-membered pyrimidine ring to represent the prerequisite V-structure in the iminopyrimidine tautomeric form. This model is subjected to incremental deprotonation and MO decomposition. The 4'-pyrimidylimine moiety, in addition to being an internal base to abstract the C2 proton, also performs as the second electron sink. Thus, the LUMOs of the thiazolium and pyrimidylimine systems working in tandem stabilize the developing charges in these transient structures, with facilitation from their HOMOs. Further, the absence of detectable amounts of the C2 carbanion in 13C2-labeled thiamin-enzyme complex by NMR is explained. Both NBO analysis and the QTAIM topological electronic properties suggest the operation of a H-bonding scheme that leads to the formation of a cryptic C2 carbanion that is not accumulated. The shielding of the carbanion by the N4'-H hydrogen bond is weakened by N1'-H deprotonation. Consequently, prior return of the N1' proton to the nearby glutamate may be the switch for streaming a timed-release of the unstable C2 carbanion to the incoming substrate.

Supramolecular networks of dinuclear copper(II): Synthesis, crystal structure and magnetic study

The complexes [Cu 2(ox)(phen) 2(H 2O) 2](NO 3) 2 ( 1), [Cu 2(sq)(pmdien) 2(H 2O) 2](ClO 4) 2 ( 2) and {[Cu 3(pdc) 3(4,4′-bipy) 1.5(H 2O) 2.25] · 2.5(H 2O)} n ( 3) [phen = 1,10-phenanthroline; pmdien = N, N, N′, N′, N″-pentamethyldiethylenetriamine; 4,4′-bipy = 4,4′-bipyridine; ox = oxalate dianion; sq = squarate dianion and pdc = pyridine 2,6-dicarboxylate] have been synthesized and characterized by X-ray single crystal structure determination, low temperature magnetic measurement and thermal study. Structure determination reveals that 1 and 2 are dinuclear copper(II) complexes bridged by oxalate and squarate dianions, respectively, while 3 is a hexanuclear species formed by three Cu(pdc)(H 2O)-(4,4′-bipy)-Cu(pdc)(H 2O) fragments, connected through long Cu–O(pdc) bonds in a centrosymmetric arrangement. In complex 1 H-bonds occurring between the coordinated water molecules and lattice nitrate anions result in eight-membered ring clusters with the concomitant formation of 1D supramolecular chain. The adjacent chains undergo π–π stacking forming a 2D architecture. In the crystal of 3 an extensive H-bonding scheme gives rise to a 3D supramolecular network. Low temperature magnetic study shows a strong antiferromagnetic coupling in 1 ( J = −288 ± 2 cm −1, g = 2.21 ± 0.01, R = 1.2 × 10 −6); and a very weak interaction in 2 and 3, the best-fit parameters being: J = −0.21 cm −1, g = 2.12 ± 0.01, R = 1.1 × 10 −6 ( 2) and J = −1.34 cm −1 ± 0.1, g = 2.14 ± 0.01, R = 1.2 × 10 −6 ( 3) ( R defines as ∑ [ ( χ M ) obs - ( χ M ) calc ] 2 / ∑ ( χ M ) obs 2 ) .

Cobalt(ii)–(dpyo)–dicarboxylate networks: unique H-bonded assembly and rare bridging mode of dpyo in one of them [dpyo = 4,4′-dipyridyl N,N′-dioxide

Polymeric networks, {[Co(dpyo)(ox)]}(n) (1), {[Co(dpyo)(fum)(H(2)O)(2)]}(n) (1) and {[Co(dpyo)(tp)(H(2)O)(2)] x [Co(H(2)O)(6)] x (tp) x (H(2)O)}(n) (3) [ox = oxalate dianion, fum = fumarate dianion, tp = terephthalate dianion and dpyo = 4,4'-dipyridyl N,N'-dioxide] have been synthesized and characterized by single crystal X-ray diffraction analyses. The structural determination reveals 1 and 2 are covalent bonded 2D networks of 4,4 topology and of these, complex 2 undergoes a H-bonding scheme resulting in a 3D supramolecular architecture. Complex 3 is a 1D coordination polymer built up by almost collinear hexacoordinated Co(ii), doubly bridged by a tp carboxylate group and a dpyo oxygen, which in combination with lattice [Co(H(2)O)(6)](2+), tp and water molecules shows an unprecedented 3D supramolecular network through H-bonding. In the polymer the dpyo shows novel mu-4,4 bridging mode towards the cobalt ion. Low temperature magnetic interaction reveals antiferromagnetic coupling in all of the complexes.

Single-sided hydroge bonding to the quinone cofactor in photosystem I probed by selective13C-labelled naphthoquinones and transient EPR

Hydrogen bonding between teh protein and one or both of the two 1,4-quinone carbonyl groups of a benzo-or naphtho-quinone constitutes a significant protein-cofactor interaction in photosynthetic reaction centers. The redistribution of charge and spin density due to a particular H-bonding scheme leaves the largest hyperfine couplings (hfc) at the highest density positions, i.e., the nuclei of the carbonyl groups directly involved in H-bonding. The spin density changes at the ring carbon positions are accessed exeripmentlaly via electron paramagnetic resonance-determined hfc tensor elements of selective13C isotope labels in one of the two carbonyl groups. Complete hfc tensor data are presented for each of the13C positions in the functional charge-separated state in reaction centers of phytosystem I (PS I) isolated from cyanobacteria. A highly asymmetric H-bonding scheme for the A1 quinone binding site due to a single dominant H-bond to one carbonyl group is confirmed. A comparison to other wel-studied quinone binding sites of other protien-cofactor systems with more complex H-bonding schemes reveals the uniqueness of the PS I site. The single-sided A1 quinone site provides an ideal test case for the various sets of density functional theory (DFT) calculations that are currently available. While the overall agreement between experimental and calculated data is quite satisfactory, a significant discrepancy is found for the high-spin-density13C position associated with the H-bonded carbonyl. The dominant hfc component (and spin density) is underestimated in the DFT calculations, not only for the high-asymmetry case in PS I, but also for other quinone binding sites with less asymmetry that result from more complex H-bonding schemes. The cosnequences and potential relevance of this finding for biological function are discussed.

Combined neutron powder and X-ray single-crystal diffraction refinement of the atomic structure and hydrogen bonding of goslarite (ZnSO4·7H2O)

AbstractThe atomic structure of synthetic, deuterated goslarite (ZnSO4·7D2O),a= 11.8176(6) Å,b= 12.0755(7) Å,c= 6.8270(4)Å, space groupP212121,Z= 4, has been refined in a combined neutron powder diffraction and X-ray single-crystal data refinement towRp1.92%,Rp1.45% andR(F2)12.66% for the neutron powder data contribution andR(F2) 8.72% for the X-ray single-crystal data contribution. Both data sets were necessary to achieve the best overall fit agreement in the Rietveld refinement and reasonable geometry within structural units. The results of this study confirm that the H-bonding scheme for goslarite is the same as that of the other epsomite group minerals. Small but significant variations of the Zn–O bond lengths can be attributed to details of the H bonds to the O atoms of the Zn octahedra. This investigation of the atomic structure and hydrogen bonding of goslarite is groundwork for future studies into phase relationships and the mechanisms of hydration and dehydration in the ZnSO4–H2O system.

BOLEITE: RESOLUTION OF THE FORMULA, K Pb26 Ag9 Cu24 Cl62 (OH)48

The crystal structure of boleite, K Pb26 Ag9 Cu24 Cl62 (OH)48, a 15.288(2) A, V 3574(1) A3, Pm 3 m , Z = 1, has been refined to an R -index of 2.2% based on 884 observed (5σ) reflections collected with Mo K α X-radiation. A new site was resolved, and site-scattering refinement showed it to be occupied by a scattering species with 19 epfu (electrons per formula unit); this result is in accord with complete occupancy of this site by K. Potassium was detected by electron-microprobe analysis, but the amount determined is only ~50% of the amount indicated by site-scattering refinement. However, the refinement results show K to be disordered within a large cage in the structure, and the electron-beam bombardment probably induces rapid migration of K within the structure. Infrared spectroscopy shows that there is no H2O present in the structure. The H-sites were determined during refinement, and a sensible H-bonding scheme results.