Crystal Structure Refinements of Legrandite, Adamite, And

Journal of Mineralogical and Petrological Sciences, Volume 111, page 35–43, 2016

Crystal structure reﬁnements of legrandite, adamite, and paradamite: The complex structure and characteristic hydrogen bonding network of legrandite

Satoshi JINNOUCHI*, Akira YOSHIASA*, Kazumasa SUGIYAMA**, Reiko SHIMURA**, Hiroshi ARIMA**, Koichi MOMMA*** and Ritsurou MIYAWAKI***

*Graduate School of Science and Technology, Kumamoto University, Kumamoto 860–8555, Japan **Institute for materials research, Tohoku University, Sendai 980–8577, Japan ***Department of Geology, National Science Museum, Tokyo 169–0073, Japan

Crystal structures of legrandite [Zn2AsO4(OH)·H2O; a = 12.8014(11), b = 7.9390(3), c = 10.2262(5) Å, β = 104.490(2)°; space group P21/c; Z = 8], adamite [Zn2AsO4(OH); a = 8.3428(11), b = 8.5664(10), c = 6.0769(8) Å; space group Pnnm; Z = 4], and paradamite [Zn2AsO4(OH); a = 5.8438(5), b = 6.7226(6), c = 5.6566(4) Å, α = 104.348(3), β = 92.320(3), γ = 76.683(3)°; space group P1; Z = 2] were investigated by single–crystal X–ray diffraction and were refined to the R1 values of 0.0212, 0.0282, and 0.0270 using 2800, 588, and 1128 unique reflections with Fo >4σ(Fo), respectively. The chemical formula of legrandite is similar to that of adamite and paradamite, except for the presence of water molecules. In the structure of legrandite, the hydrogen atoms are distributed among the two hydroxyl and the two water molecule positions. On the basis of bond valence calculations, the hydrogen bonding in legrandite can be classified into three types: (1) one acceptor with linear normal hydrogen bonding (Type–A), (2) two acceptors with linear hydrogen bonding and one excess weak hydrogen bonding (Type–B), and (3) several acceptors with one linear hydrogen bondings and several weak hydrogen bondings by weak electrostatic interactions (Type–C). The variety of hydrogen bonding interactions provides structural stability to legrandite. The Zn3–O1 bond shows a remarkable distance of 2.341(2) Å, which is ascribed to the three–dimensional periodicity of the complex mineral structure. The local structures of adamite and paradamite violate a fundamental crystallographic law with respect to the cation coordination number and unit cell volume. The crystal structures of legrandite and paradamite are characterized by proton transfer tunnels running along the crystal axes.

Keywords: Legrandite, Adamite, Paradamite, Crystal structure, Hydrogen bonding

INTRODUCTION different coordination environments: Zn1O4(OH)2 octahedral, Zn2O4(OH) trigonal bipyramidal, Zn3O3(OH)2 Minerals contain water molecules in the form of hydrates, trigonal bipyramidal, and Zn4O3(H2O)2 trigonal bipyra- substituting water, zeolite water, and interlayer water, midal geometries. which are tightly hydrogen–bonded to cations. It is im- The structure of legrandite has been extensively portant to clarify the role of water molecules, and espe- studied by several authors (Drugman and Hey, 1932; Fin- cially that of their hydrogen bonding interactions, in the ney, 1963; Desautels and Clarke, 1963; McLean et al., crystal structure of minerals. The chemical formula of the 1971). However, the positions of the hydrogen atoms zinc arsenate mineral legrandite [Zn2AsO4(OH)·H2O] is and the anisotropic thermal displacement parameters similar to that of adamite [Zn2AsO4(OH)] and paradamite have not yet been determined. Recently, Hawthorne et [Zn2AsO4(OH)], except for the presence of water mole- al. (2013) successfully performed structure refinement cules. In legrandite, zinc ions are distributed among four and identified the positions of the hydrogen atoms in fi doi:10.2465/jmps.141216 the crystal structure of legrandite. Two interesting nd- S. Jinnouchi, [email protected] Correspond- ings emerged from their study. First, only the Zn3–O1 ing author bond showed an unusual length of 2.346(2) Å, which is 36 S. Jinnouchi, A. Yoshiasa, K. Sugiyama, R. Shimura, H. Arima, K. Momma and R. Miyawaki an extremely long Zn–O distance as compared with the mite, and paradamite were 16.01, 18.52, and 19.19 mm−1, expected value of 2.12 Å reported by Shannon (1976). respectively. The absorption correction was performed Second, the bond valence sum of O1 (1.856 vu) was using the integration method on the basis of the observed found to be significantly smaller than the ideal value of arbitrary shape of the specimens. The initial structures 2.00 vu. In this study, we examined the structure of le- were solved by a direct method, and 2800, 588, and grandite in order to elucidate the reasons for the long 1128 of unique reflections with Fo >4σ(Fo) were then used Zn3–O1 distance and the unsaturated bond valence sum for full–matrix least–square refinement. of O1. Moreover, we confirmed the presence of hydrogen bonding interactions in legrandite. The electrostatic con- Crystal structure refinement and determination of hy- tribution and compensation between O1 and the hydro- drogen atom positions gen atoms are also discussed. Adamite and paradamite are members of the olivenite All refinements were carried out using the SHELX97 and tarbuttite groups of minerals, respectively. The struc- program (Sheldrick, 1997). After the least–square refine- ture of adamite has been investigated since the 1930s ments without hydrogen atoms, the R1 indexes (= Σ||Fo| − (Kokkoros, 1937; Hill, 1976; Hawthorne, 1976; Kato |Fc||/Σ|Fo|) were converged to less than 0.03 using aniso- and Miura, 1977) and was confirmed to be similar to that tropic temperature factors. Difference Fourier calcula- of andalusite (Al2SiO5). Paradamite, a polymorph of ada- tions were performed to locate the hydrogen atoms in mite, is isostructural with tarbuttite [Zn2PO4(OH)] (Swit- the structures. Peaks attributable to hydrogen atoms could zer, 1956; Finney, 1966) and has also been previously be detected. Figure 1 shows the difference Fourier maps studied by Kato and Miura (1977) and Bennett (1980). around the hydrogen and oxygen atoms (O9 and O11) in In this work, we investigated the crystal structures of legrandite. The highest peaks (ρ ≥1.0 e/Å3) within the adamite and paradamite and we compared the hydrogen distances of 1.0 Å from an oxygen atom were used to bonding interactions observed in these minerals to those estimate the hydrogen atom positions. The determination observed in legrandite, a related structure with different of the hydrogen atom positions was performed as follows: coordination environments. (1) candidate peaks were selected from the difference Fourier maps, (2) the crystal structure was refined by EXPERIMENTS the least–squares method including hydrogen atoms, and (3) the crystallographic validity was finally assessed by Materials and data collection the hydrogen atom positions obtained. The crystal structures were illustrated using the computer program VESTA Single crystals of legrandite, adamite, and paradamite (Monma and Izumi, 2011). The structure refinement data suitable for single–crystal X–ray diffraction analysis were of legrandite, adamite, and paradamite are listed in Table carefully selected from the specimens of the Ojuela Mine, 1. The positional parameters and the isotropic/anisotropic Mapimi, Durango, Mexico. The crystals of legrandite, thermal displacement parameters for legrandite, adamite, adamite, and paradamite were pale yellow, yellow to col- and paradamite are given in Tables 2, 3, and 4, respective- orless, and ideally white, respectively. The chemical com- ly. Their selected interatomic distances and angles and positions of the samples were determined by JEOL scan- their results of bond valence sum calculation are listed ning electron microscope (JSM–7001F) and Oxford en- in Tables 5–10. ergy dispersive X–ray analyzer (INCA SYSTEM). Only phosphorus and iron were detected as impurities (P2O5 RESULTS AND DISCUSSION ≤0.85 wt%, Fe2O3 ≤1.72 wt%), which are negligible for crystal structure analysis; thus, in this study, ideal chemi- Brief description of the structures cal compositions were used for structure refinement. Crystallographic data were collected on a Rigaku X– In legrandite, there are two As5+ tetrahedral sites and four 2+ ray diffractometer (RAPID) with an imaging plate (graph- Zn sites forming Zn1O4(OH)2 octahedral, Zn2O4(OH) ite–monochromatized MoKα radiation, λ = 0.71069 Å), trigonal bipyramidal, Zn3O3(OH)2 trigonal bipyramidal, at Tohoku University. Systematic absence conditions of and Zn4O3(H2O)2 trigonal bipyramidal geometries. As legrandite, adamite, and paradamite supported the space a result, the Zn3–O1 bond showed an unusual length groups of P21/c, Pnnm, and P1, respectively. A total of of 2.314(2) Å, a finding similar to a previous report 11617, 2916, and 2879 reflections were collected. The (Hawthorne et al., 2013). The structures of adamite and intensities were corrected for Lorentz and polarization paradamite contain one As5+ site and two distinct Zn2+ factors. The absorption coefficients of legrandite, ada- sites. In both adamite and paradamite, the As5+ site shows Crystal structure refinements of legrandite, adamite, and paradamite 37

Figure 1. Difference Fourier maps a- round the hydrogen and oxygen atoms of the (a) water molecule (O9, H91, and H92) and (b) hydroxyl anion (O11 and H11) in legrandite. The contour interval is 0.2 e/Å3.

a slightly distorted AsO4 tetrahedral coordination. In ada- atom reflects the bonding character, such as donor, accep- mite, the Zn1 site shows an octahedral coordination with tor, or weak electrostatic hydrogen acceptor. In legrandite, four O2− and two (OH)− groups, whereas the Zn2 forms a three types of hydrogen bonding can be considered: (1) five–coordinated polyhedron, which can be described as a one acceptor with normal or weak hydrogen bonding trigonal bipyramid with four O2− and one (OH)− group. In (Type–A: around H91 and H101), (2) two acceptors with paradamite, the Zn1 and Zn2 sites show trigonal bipyra- linear hydrogen bonding and one excess weak hydrogen midal coordination by three O2− and two (OH)− groups bonding (Type–B: H111 and H121), and (3) several ac- and four O2− and one (OH)− groups, respectively. Thus, ceptors with one linear hydrogen bonding and several among the three structures, the structure of legrandite is weak hydrogen bondings by weak electrostatic interac- the most complex. Paradamite has a smaller lattice volume per formula unit, and therefore a higher density phase, than adamite. The coordination number of the Table 1. Experimental details and crystallographic data two Zn sites is five in paradamite and six in adamite. Generally, a high–density phase adopts a structure with a high coordination number for cations; thus, the local structures observed around the Zn cations in adamite and paradamite are contrary to the fundamental crystallographic law.

Bond valence sum calculation and details of hydrogen bonding interactions

Six normal hydrogen acceptor bonds were reported by Hawthorne et al. (2013): H1…O8, H2…O8, H3…O8, H4…O4, H5…O4, and H6…O11. The low O1 valence value of 1.856 vu suggests an additional electrostatic interaction between hydrogen and oxygen atoms. In a hydrogen bonding system, O–H…O, the nature of the hydrogen to donor oxygen bond is covalent, whereas that of the hydrogen to acceptor oxygen bond is electrostatic. Brown (1976) reported that the H…O distance in a weak hydrogen acceptor bond ranges between 2.3 and 3.1 Å and the O–H…O angles between 80° and 120°. We investigated the electrostatic compensation in legrandite on the basis of bond valence calculations. Table 8 shows the bond valence sum calculations according to Brown’s model. The bond valence for each hydrogen 38 S. Jinnouchi, A. Yoshiasa, K. Sugiyama, R. Shimura, H. Arima, K. Momma and R. Miyawaki

Table 2. Positional parameters and isotropic/anisotropic thermal displacement parameters for legrandite

Table 3. Positional parameters and isotropic/anisotropic thermal displacement parameters for adamite

Table 4. Positional parameters and isotropic/anisotropic thermal displacement parameters for paradamite Crystal structure reﬁnements of legrandite, adamite, and paradamite 39

Table 5. Selected interatomic distances (Å) and angles (°) for legrandite

tions (Type–C: H92 and H122). The variety of hydrogen bonding interactions provides structural stability to the complex structure of legrandite. Additional weak hydrogen acceptor bondings with a bond valence sum that is consistent with Brown’s model were investigated. As shown in Table 8, the bond valence sum (1.860 vu) for O1 is signiﬁcantly smaller than the ideal value of 2.00 vu, presumably because of the remarkably long Zn3–O1 bond distance of 2.341(2) Å (Table 5). That is, the numerous water molecules and several structural misﬁts around the O1 atom of legrandite cause structural incompatibility. In legrandite, besides O1, the oxygen atoms O3, O8, O9, O11, and O12 were found to be involved in weak hydrogen acceptor bondings (electrostatic interactions). The bond distances and angles, including hydrogen bonding, are listed in Table 5. Figure 2 shows the crystal structure around the H91 atoms. The H91…O11 hydrogen bond is a typical linear hydrogen bond. The local structure around the H101 and H111 atoms is illustrated in Figure 3a. The H101 and H111 atoms are present as (OH)− groups. The H111 acts as double acceptor, in a linear hydrogen bonding (H111…O8) and in a weak hydrogen bonding (H111…O1). The hydrogen bonding distance for O11–H111…O1 is similar to that for O10– H101…O8 (Table 5). 40 S. Jinnouchi, A. Yoshiasa, K. Sugiyama, R. Shimura, H. Arima, K. Momma and R. Miyawaki

Table 6. Selected interatomic distances (Å) and angles (°) for adamite

Table 7. Selected interatomic distances (Å) and angles (°) for paradamite

Table 8. Bond valence sum calculation for legrandite

Table 10. Bond valence sum calculation for paradamite

Table 9. Bond valence sum calculation for adamite Crystal structure reﬁnements of legrandite, adamite, and paradamite 41

Figure 2. Crystal structure of legrandite parallel to the [001] direction. The normal hydrogen acceptor bonding is shown as a solid line. The black dashed squares indicate the one–dimensional tunnels.

Figure 3. Local structure around the (a) H101 and H111 atoms and (b) H121 atom in legrandite. The normal hydrogen acceptor bonding and the weak electrostatic interaction are shown as solid and dashed lines, respectively.

Figure 4. Local structure around the (a) H122 and (b) H92 atoms in legrandite. The O9 and O12 donor oxygen atoms are coordinated to the Zn4 atoms forming a Zn4O3(H2O)2 trigonal bipyramidal geometry. The normal hydrogen acceptor bonding and the excess weak electrostatic interaction are shown as solid and dashed lines, respectively. 42 S. Jinnouchi, A. Yoshiasa, K. Sugiyama, R. Shimura, H. Arima, K. Momma and R. Miyawaki

The H91, H92, H121, and H122 atoms are bound to is well–known in the structure of adamite and paradamite. oxygen atoms as a water molecule. The coordination en- In paradamite, the coordination environment around the vironment around the H121 atom is displayed in Figure hydrogen atoms results in a low symmetrical geometry. 3b. The H121 atom acts as double acceptor, in a linear hydrogen bonding (H121…O8) and in a weak hydrogen Hydrogen bonding and proton transfer bonding (H121…O11). Because the hydrogen bonds around H122 and H92 are of Type–C, several weak hy- The three minerals have the same chemical formula, ex- drogen acceptor bondings are observed in addition to the cept for the number of water molecules. The structural linear hydrogen bondings H122…O4 and H92…O4. Fig- complexity of legrandite is presumably due to the pres- ures 4a and 4b show the coordination environments ence of two crystallographically inequivalent water mole- around the H122 and H92 atoms, respectively. cules. The structures of adamite and paradamite, which Tables 9 and 10 present the bond valence sum cal- contain no water molecules, show inﬁnite edge–sharing culations for adamite and paradamite, respectively. Fig- chains of Zn polyhedra, consisting of three–dimensional ures 5 and 6 illustrate the coordination environments frameworks. In legrandite, on the other hand, the water around the H atoms in adamite and paradamite, respec- molecules prevent the formation of inﬁnite edge–sharing tively. In adamite, two H…O4 bifurcated hydrogen bond- chains and provide structural stability by forming a com- ings are formed by the hydrogen atoms located on a plicated hydrogen–bonding network with weak electro- mirror plane. In paradamite, the distance and angles of static interactions. The Zn3–O1 bond distance in legran- the H…O1 hydrogen bond are similar to those of the dite must be extremely long in order to satisfy the three– H…O1’ interaction, a bifurcated hydrogen bonding that dimensional periodicity of the structure. Among the three minerals, legrandite shows the highest proton conductivity and the lowest thermal stability (Desautels and Clarke, 1963). There are various types of hydrogen bonding in its structure, and tunnels parallel to the [001] direction can be clearly observed around the H91 atom (Fig. 2). A proton, H+, can easily move through the tunnels and, presumably, the fastest proton transfer occurs through this channel, although there are many tunnels in the structure. In paradamite, a tunnel system parallel to the [100] direction can be observed (Fig. 6). Inter- estingly, the structure of paradamite has larger tunnels than that of adamite despite its smaller lattice volume.

ACKNOWLEDGMENTS Figure 5. Local structure around the hydrogen atom and hydrogen bond in adamite. The normal bifurcated hydrogen acceptor The preliminary experiment was performed under the bonding is shown as a solid line. auspices of Photon Factory (PAC No. 2013G063).

Figure 6. Crystal structure of paradamite parallel to the [100] direction. The normal bifurcated hydrogen acceptor bonding is shown as a solid line. The black dashed squares indicate the one–dimensional tunnels. Crystal structure reﬁnements of legrandite, adamite, and paradamite 43

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