Determination of orientational ordering of hydroxy groups in kulanite between 120-353 K using single-crystal X-ray diffraction

Abstract

We conducted single-crystal X-ray diffraction experiments on kulanite [Ba(Fe²⁺, Mn²⁺, Mg)₂(Al, Fe³⁺)₂(PO₄)₃(OH)₃] to investigate the potential orientational ordering of its hydroxy groups. Structural refinements showed no sign of a phase transition between 120 and 353 K. Additionally, the orientation of the hydroxy group was determined uniquely along the c-axis for the measured temperature range of 120-353 K.

INTRODUCTION

Kulanite is a barium iron aluminum phosphate with the chemical formula Ba(Fe²⁺, Mn²⁺, Mg)₂(Al, Fe³⁺)₂(PO₄)₃(OH)₃ (Mandarino and Sturman, 1976). It belongs to the Bjarebyite group characterized by the coexistence of heavy elements (such as Ba, Sr, and Pb) and transition metals (Moore and Araki, 1974; Strunz and Nickel, 2001; Elliott and Kampf, 2020). The iron in kulanite exists as divalent and trivalent cations that form chains of edge- and corner-sharing octahedra with the oxygen atoms (Strunz and Nickel, 2001). Some oxygen atoms exist as hydroxy (OH) groups, whose orientational disorder is one of the structural characteristics of kulanite (Cooper and Hawthorne, 1994). There are two types of OH groups (Fig. 1). One of them (O9-H2) forms a typical hydrogen bond with oxygen atom O3, with a hydrogen-bonded O9-O3 length of 2.66 Å. The other hydroxy group (O8-H1) coordinating Ba and the trivalent transition metals forms a substantially weak hydrogen bond with oxygen atom O6, with a hydrogen-bonded O8-O6 length of 3.35 Å (Cooper and Hawthorne, 1994). Hereafter, we refer to this hydroxy group as the ‘free hydroxy group (or OH)’. In addition, the free hydroxy group is orientationally disordered against the mirror plane passing through the oxygen atom site (Cooper and Hawthorne, 1994). The disordered state has not been extensively studied; however, within the Bjarebyite group of minerals, this orientational disorder of the hydroxy groups has only been previously reported for kulanite (Elliott and Willis, 2011; Bowman et al., 2013). If this state is derived from a dynamical process, such as thermal fluctuation, then temperature might induce an orientational disorder-order phase transition similar to that reported for hydroxyapatite (Hochrein et al., 2005). This type of phase transition can induce intriguing changes in the electrical properties of minerals (e.g., pyro- or ferroelectricity; see Tofail et al., 2005). Thus, we performed single-crystal X-ray diffraction examinations of kulanite under varying temperature conditions to investigate the potential orientational ordering of the hydroxy groups in kulanite.

Figure 1. Crystal structure of kulanite with descriptions of the types of elements, and hydroxy groups O8-H1 and O9-H2 in addition to their related oxygen atoms O3 and O6. The crystal structures were drawn by VESTA developed by Momma and Izumi (2011).

MATERIALS AND METHODS

Our kulanite sample was taken from Rapid Creek, Yukon Territory, Canada, the same locality for the sample used by Cooper and Hawthorne (1994). A blue-green, plate-shaped specimen with a diameter of approximately 2 mm. A single 0.05 × 0.07 × 0.08 mm crystal was attached to a glass fiber (φ25 µm) and mounted on a Rigaku XtaLAB Synergy-S diffractometer equipped with a HyPix-6000HE hybrid photon counting (HPC) detector and Mo microfocus-sealed X-ray source. The temperature was controlled by a liquid-nitrogen cryostream (Rigaku, GN2-SN), and the sample temperature was estimated from the calibration data measured in advance using a K-type thermocouple. Experiments were conducted at 120, 220, 276, room temperature (RT, ~ 297 K), and 353 K. The X-ray diffraction data at each temperature condition were collected for a reciprocal whole sphere (redundancy is about 3) with a resolution of 0.6 Å, except for the measurement at 353 K, where a resolution of 0.7 Å was used. The data were absorption-corrected using the CrysAlis program (Rigaku Oxford Diffraction, 2018). Cell parameters were also determined by this program.

STRUCTURAL REFINEMENT

Least-squares refinement was performed using the SHELXL software program (Sheldrick, 2015) implemented in WinGX (Farrugia, 2012). The scattering factors for neutral atoms and the anomalous dispersion coefficients were obtained from the International Tables for Crystallography Volume C (1992). The chemical composition of our sample was determined using the structural refinement of the obtained data at 120 K and was fixed in consecutive refinements with the other data sets. For the M1 site occupied by Fe²⁺, Mg²⁺, and Mn²⁺, Cooper and Hawthorne (1994) reported that the occupancy ratio of Mn²⁺/Fe²⁺ was approximately 7%, using a sample from the same locality. Since a similarity of the atomic scattering factor of Fe and Mn due to the neighboring of these atoms in the periodic table, Fe at the M1 site represents Fe²⁺ + Mn²⁺ in our refinement. Difference between their anomalous dispersion terms were discarded for the low concentration of Mn. Details of the substitutions in kulanite have been reported by Cooper and Hawthorne (1994). We should note that the Fe²⁺, Mg²⁺, and Mn²⁺ ions were attributed to the M2 site, occupied by Al³⁺ and Fe³⁺ in this paper, in Cooper and Hawthorne (1994). However, the assignment of metal ions was switched by the authors in a crystal structure database managed by the Mineralogical Society of America and the Mineralogical Association of Canada in 2006, and this paper follows the new assignment. In the structural refinements, the atomic coordinates and site occupancy of non-hydrogen atoms were refined using the anisotropic displacement model. Hydrogen atoms were finally introduced based on the residual peaks. The hydrogen atom coordinates were treated with a riding model, and their isotropic displacement parameters were constrained to 1.5 times of the U_eq of the adjacent oxygen atoms. The initial atomic coordinates for the data obtained at the lowest temperature (120 K) were taken from Cooper and Hawthorne (1994). For data collected at other temperatures, the initial atomic coordinates were based on the refinement result for 120 K data. In addition, we comment on the space group of kulanite. Figure 2 shows the intensity distribution on slices in reciprocal space reconstructed from the intensity data obtained at 120 K and RT. There was no sign of superstructure reflection accompanied with orientational ordering of the free OH even at 120 K. However, a few reflections violated the reflection condition of P2₁/m (0k0: k = 2n) at all the temperatures examined, e.g., 030 and 050 (they are obscure in Fig. 2); thus, further structural refinement using a lower symmetry without a 2₁ screw axis was conducted. Nevertheless, there was no significant improvement in the refinement, and we used P2₁/m as the space group of kulanite, similar to that by Cooper and Hawthorne (1994).

Figure 2. Intensity distribution of h0l and 0kl reciprocal space reconstructed by the present intensity measurement in 120 K and RT.

RESULTS AND DISCUSSION

Table 1 shows the structural refinement details of the kulanite from Rapid Creek, Yukon Territory, Canada. The cell parameters of kulanite decrease with lowering temperature, and from the temperature change, there is no sign of phase transition in kulanite. The chemical composition of the kulanite sample was determined to be Ba(Fe_0.82, Mg_0.18)₂(Al_0.91, Fe_0.09)₂(PO₄)₃(OH)₃. Tables 2 and 3 show the structural and anisotropic displacement parameters of the sample obtained at 120 K (the other temperature data are listed in the Supplementary Tables S1-S8; available online from https://doi.org/10.2465/jmps.220701). Our refined crystal structure was almost the same as that reported by Cooper and Hawthorne (1994), except for the spatial distribution of free OH. Figure 3 shows the crystal structure of kulanite and the difference Fourier maps obtained from the results of the structural refinements before introducing hydrogen atoms. Although Cooper and Hawthorne (1994) reported that the orientation of free OH is disordered off the mirror plane, our sample shows no indication of such behavior, and the free hydroxy group lies on the mirror plane, as shown in Figure 3A. In addition, this spatial distribution shows no significant changes within the measured temperature region.

Table 1. Structure refinement details of kulanite from Rapid Creek, Yukon, Canada

Chemical formula	Ba(Fe0.82, Mg0.18)2(Al0.91, Fe0.09)2(PO4)3(OH)3
Wavelength	0.71073 Å
Device	XtaLAB Synergy-S
Temperature	120 K	220 K	276 K	RT (~ 297 K)	353 K
Crystal system	Monoclinic	Monoclinic	Monoclinic	Monoclinic	Monoclinic
Space group	P21/m	P21/m	P21/m	P21/m	P21/m
Cell constants	a = 9.0356(2) Å	a = 9.0452(2) Å	a = 9.0440(2) Å	a = 9.0518(2) Å	a = 9.0537(1) Å
	b = 12.1065(2) Å	b = 12.1228(2) Å	b = 12.1275(3) Å	b = 12.1362(3) Å	b = 12.1410(1) Å
	c = 4.9329(1) Å	c = 4.9358(1) Å	c = 4.9367(1) Å	c = 4.9411(1) Å	c = 4.9415(1) Å
	β = 100.421(2)°	β = 100.443(2)°	β = 100.431(2)°	β = 100.443(2)°	β = 100.437(1)°
Volume (Å3)	530.71(2)	532.26(2)	532.51(2)	533.81(2)	534.19(1)
Max. 2-theta (resolution)	75.190° (0.6 Å)	74.934° (0.6 Å)	75.280° (0.6 Å)	75.964° (0.6 Å)	66.110° (0.7 Å)
Index ranges	−15 ≤ h ≤ 15	−15 ≤ h ≤ 14	−15 ≤ h ≤ 14	−14 ≤ h ≤ 15	−13 ≤ h ≤ 13
	−16 ≤ k ≤ 20	−10 ≤ k ≤ 20	−10 ≤ k ≤ 20	−12 ≤ k ≤ 20	−18 ≤ k ≤ 18
	−8 ≤ l ≤ 7	−8 ≤ l ≤ 8	−8 ≤ l ≤ 7	−8 ≤ l ≤ 8	−7 ≤ l ≤ 7
Measured reflections	8052	9819	8494	9532	15459
Rint / Rsigma	0.0196 / 0.0228	0.0261 / 0.0245	0.0224 / 0.0242	0.0205 / 0.0208	0.0273 / 0.0153
Data / parameters	2793 / 117	2763 / 113	2781 / 113	2820 / 113	1975 / 113
Goodness-of-fit in F2	1.121	1.075	1.105	1.109	1.163
R indices I > 2σ(I)	0.0168	0.0171	0.0176	0.0161	0.0138
R indices (all data)	0.0177	0.0185	0.019	0.0176	0.0145
Δρmax / Δρmin (eÅ−3)	0.843 / −0.830	0.717 / −0.777	0.670 / −0.807	0.812 / −0.831	0.493 / −0.468
weight: w = 1/[σ2(Fo2) + (AP)2 + BP], where P = (Fo2 + 2Fc2)/3
	A = 0.0146, B = 0.234	A = 0.0128, B = 0.323	A = 0.0152, B = 0.188	A = 0.0135, B = 0.302	A = 0.0147, B = 0.381

Table 2. Structural parameters of kulanite from Rapid Creek, Yukon, Canada, obtained at 120 K

Atom	Occupation	x	y	z	Ueq (Å2)
Ba	Ba	0.54724(2)	3/4	0.74080(2)	0.00412(3)
M1	Fe 0.822(2) Mg 0.178	0.29556(2)	−0.10916(2)	0.20665(5)	0.00427(5)
M2	Al 0.913(2) Fe 0.087	0.09110(4)	0.40031(3)	0.12838(8)	0.00325(9)
P1	P	0.15635(5)	3/4	0.68477(10)	0.00293(7)
P2	P	0.33258(3)	0.44141(3)	0.70445(7)	0.00329(6)
O1	O	0.2791(2)	3/4	0.9448(3)	0.0063(2)
O2	O	0.2310(2)	0.75000	0.4316(3)	0.0047(2)
O3	O	0.0602(1)	0.64573(8)	0.6860(2)	0.0055(2)
O4	O	0.3691(1)	0.55630(8)	0.6123(2)	0.0058(2)
O5	O	0.2580(1)	0.45172(8)	0.9660(2)	0.0062(2)
O6	O	0.2263(1)	0.38165(8)	0.4695(2)	0.0066(2)
O7	O	0.4721(1)	0.36905(8)	0.7871(2)	0.0061(2)
O8	O	0.1236(2)	0.25000	0.0077(3)	0.0057(2)
O9	O	0.0587(1)	0.55741(8)	0.19000(2)	0.0055(2)
H1	H	0.13170	1/4	0.15905	0.009
H2	H	0.05144	0.57887	0.34388	0.008

Table 3. Anisotropic displacement parameters (Ų) of kulanite from Rapid Creek, Yukon, Canada, obtained at 120 K

Atom	U11 (Å2)	U22 (Å2)	U33 (Å2)	U23 (Å2)	U13 (Å2)	U12 (Å2)
Ba	0.00348(4)	0.00444(5)	0.00445(5)	0	0.00072(3)	0
M1	0.00336(8)	0.00367(9)	0.0057(1)	−0.00033(6)	0.00054(6)	−0.00003(6)
M2	0.0029(1)	0.0031(2)	0.0038(2)	−0.0005(1)	0.0006(1)	0.0003(1)
P1	0.0023(2)	0.0032(2)	0.0031(2)	0	0.0003(1)	0
P2	0.0033(1)	0.0030(1)	0.0035(1)	−0.00048(9)	0.00052(9)	−0.00035(9)
O1	0.0043(5)	0.0095(6)	0.0047(6)	0	−0.0005(4)	0
O2	0.0056(5)	0.0045(5)	0.0044(6)	0	0.0018(4)	0
O3	0.0059(3)	0.0041(3)	0.0073(4)	−0.0005(3)	0.0029(3)	−0.0013(3)
O4	0.0062(3)	0.0037(3)	0.0075(4)	−0.0012(3)	0.0012(3)	−0.0001(3)
O5	0.0061(3)	0.0081(4)	0.0049(4)	0.0000(3)	0.0024(3)	0.0001(3)
O6	0.0067(4)	0.0062(4)	0.0063(4)	0.0016(3)	−0.0008(3)	0.0009(3)
O7	0.0047(3)	0.0059(4)	0.0076(4)	−0.0017(3)	0.0008(3)	−0.0026(3)
O8	0.0063(5)	0.0060(5)	0.0051(6)	0	0.0016(4)	0
O9	0.0061(3)	0.0061(4)	0.0044(4)	0.0024(3)	0.0014(3)	0.0009(3)

Figure 3. (A) Difference Fourier map of kulanite in the mirror plane (x, 3/4, z) and the plane through the free hydroxy group (O8-H1) parallel to the b-axis (measured at RT). (B) Difference Fourier maps at 120 K, RT (~ 297 K), and 353 K in the plane through the free OH parallel to the b-axis described based on the results of the structural refinements before introducing hydrogen atoms.

Figure 4 shows the temperature dependence of the distances between the hydrogen-bonded O9-O3 and substantially weak hydrogen-bonded O8-O6. Both distances were lengthened by the expansion of kulanite at higher temperatures, and they increased 0.45 and 0.28% from 120 to 353 K. The O9-H2 and O8-H1 (free OH) distances of kulanite are approximately 0.82-0.83 Å. There is no significant temperature dependence; at 120 K, the O9-H2 and O8-H1 distances were 0.8388 and 0.8160 Å, respectively.

Figure 4. Temperature dependence of distances between the hydrogen-bonded O9-O3 and the substantially weak hydrogen-bonded O8-O6.

Finally, although we refer to hydroxy O8-H1 as ‘free OH’, we comment on the hydrogen bond of this hydroxy group. Cooper and Hawthorne (1994) suggested that when hydrogen atom H1 is disordered off the mirror plane, the distance between H1 and the next-nearest-neighbor oxygen atom O6 decreases. Frost et al. (2013) reported the Raman and infrared spectra of kulanite over the 2600-4000 cm⁻¹ region, which were divided into two OH stretching bands: one showed a sharp peak at approximately 3530 cm⁻¹ and the other showed a broad peak at a lower frequency of approximately 3200 cm⁻¹. The spectrum’s shape resembles those obtained for solvents in which free (isolated) OH and hydrogen-bonded OH coexist (Singh et al., 2022). Additionally, free OH shows a higher frequency of stretching than hydrogen-bonded OH (Singh et al., 2022) because of the weakening of the covalent bond along with the formation of a hydrogen bond. Considering this contrast, we can conclude that free and hydrogen-bonded OH coexist within kulanite. Additionally, this description might be applied to other Bjarebyite group minerals, considering the similarity of their crystal structures. In this context, the difference in bond strength of O9-H2 and O8-H1 would be reflected in the degree of increase of the O9-O3 and O8-O6 distances through thermal expansion (Fig. 4): respectively, from 2.668(2) Å at 120 K to 2.680(2) Å at 353 K, and from 3.367(2) Å at 120 K to 3.377(2) Å at 353 K.

CONCLUSIONS

Single-crystal X-ray diffraction measurements of kulanite revealed that orientational ordering of the free hydroxy group does not occur in the temperature range of 120-353 K. Additionally, the orientation of OH is uniquely determined on the mirror plane as well as the other Bjarebyite group minerals.

ACKNOWLEDGMENTS

This research was supported by JSPS KAKENHI Grant Numbers JP18H05456, JP20H00189, and JP22K14750.

SUPPLEMENTARY MATERIALS

Supplementary Tables S1-S8 are available online from https://doi.org/10.2465/jmps.220701.

REFERENCES

•  Bowman,  M.G.,  Downs,  R.T. and  Yang,  H. (2013) Penikisite, BaMg₂Al₂(PO₄)₃(OH)₃, isostructural with bjarebyite. Acta Crystallographica, E69, i4-i5.
•  Cooper,  M. and  Hawthorne,  F.C. (1994) Refinement of the crystal structure of kulanite. The Canadian Mineralogist, 32, 15-19.
•  Elliott,  P. and  Willis,  A.C. (2011) The crystal structure of perloffite. Mineralogical Magazine, 75, 317-325.
•  Elliott,  P. and  Kampf,  A.R. (2020) Plumboperloffite, IMA 2020-007. CNMNC Newsletter No. 55; Mineralogical Magazine, 84, 485-488.
•  Farrugia,  L.J. (2012) WinGX and ORTEP for Windows: an update. Journal of Applied Crystallography, 45, 849-854.
•  Frost,  R.L.,  Lopez,  A.,  Xi,  Y.,  Granja,  A. and  Scholz,  R. (2013) Vibrational spectroscopic characterization of the phosphate mineral kulanite Ba(Fe²⁺, Mn²⁺, Mg)₂(Al, Fe³⁺)₂(PO₄)₃(OH)₃. Spectrochimica Acta Part A, 115, 22-25.
•  Hochrein,  O.,  Kniep,  R. and  Zahn,  D. (2005) Atomistic simulation study of the order/disorder (Monoclinic to Hexagonal) phase transition of hydroxyapatite, Chemistry of Materials, 17, 1978-1981.
• International Tables for Crystallography Volume C: Mathematical, physical and chemical tables (1992) Kluwer Academic Publishers, Dordrecht.
•  Mandarino,  J.A. and  Sturman,  B.D. (1976) Kulanite, a new barium iron aluminum phosphate from the Yukon Territory, Canada. The Canadian Mineralogist, 14, 127-131.
•  Momma,  K. and  Izumi,  F. (2011) VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data. Journal of Applied Crystallography, 44, 1272-1276.
•  Moore,  P.B. and  Araki,  T. (1974) Bjarebyite, Ba(Mn, Fe)²⁺₂Al₂(OH)₃[PO₄]₃: Its atomic arrangement. American Mineralogist, 59, 567-572.
• Rigaku Oxford Diffraction: CrysAlis Pro. (2018) Rigaku Oxford Diffraction Ltd. Yarnton, England.
•  Sheldrick,  G.M. (2015) Crystal structure refinement with SHELXL. Acta Crystallographica, C71, 3-8.
•  Singh,  S.,  Majer,  M.,  Czarnecki,  M.A.,  Morisawa,  Y. and  Ozaki,  Y. (2022) Solvent effect on assembling and interactions in solutions of phenol: Infrared spectroscopic and density functional theory study. Applied Spectroscopy, 76, 28-37.
• Strunz, H. and Nickel, E.H. (2001) Strunz mineralogical tables (9th Edition). 8.BH.20, Phosphates. pp.457, E. Schweizerbart’sche Verlagsbuchhansdlung, Germany.
•  Tofail,  S.A.M.,  Haverty,  D.,  Stanton,  K.T. and  McMonagle,  J.B. (2005) Structural order and dielectric behavior of hydroxyapatite. Ferroelectrics, 319, 117-123.