INTRODUCTION
Hydrous copper arsenate, Cu3AsO4(OH)3, clinoclase is transparent greenish-deep-blue in colour and forms bladed or columnar crystals in the weathered zones of copper deposits. It exhibits perfect cleavage parallel to (100) plane. The crystal structure was determined by Ghose et al. (1965). The structure, except for hydrogen atom positions, was refined by Eby and Hawthorne (1990). They compared the degree of distortion of five-coordinate Cu2+ sites in clinoclase with other copper minerals, based on classification of tetragonal pyramidal and trigonal bi-pyramidal coordinations. They concluded that the variations in the Cu-O distances generated in the tetragonal pyramidal configuration are larger than those in the trigonal bi-pyramidal configuration. However, they did not mention particularly large variations in Cu-O distances in clinoclase.
Callaghanite, Cu2Mg2(CO3)(OH)6·2H2O, is transparent bluish-deep-purple in colour and was discovered near intrusive peridotite dikes in magnesite and dolomite (Beck and Burns, 1954). The mineral has a complex chemical composition with carbonate, hydroxide, and water molecules. The crystal structure of callaghanite was determined by Brunton et al. (1958) and the atomic coordinates, except for hydrogen atoms, were refined by Brunton (1973). Covalent, ionic, van der Waals, and hydrogen bonds form the complex crystal structure of callaghanite, while the variation in the Cu-O distances is insignificant.
The Cu2+ ions in clinoclase and callaghanite adopt a characteristic five-coordinate tetragonal pyramidal environment (4 + 1). The Cu2+ ions in clinoclase and callaghanite are located near the center of the square basal plane of the tetragonal pyramid, rather than in the exact center of a five-coordinate environment. The Cu square bases of tetragonal pyramid in clinoclase are highly distorted with extremely large variations in bond distances. In contrast, the Cu square bases show little variation in Cu-O bond distances in chemically complex callaghanite.
The Cu2+ ion can take either a square planar (4 + 0) or a six-coordinate bipyramidal (4 + 2) coordination environment (Wells, 1962; Åsbrink and Norrby, 1970; Effenberger, 1977; Burns and Hawthorne, 1996; Miletich et al., 1997). Cu2+ in CuO tenorite forms a square (rectangle) planar coordination (1.961 × 2 and 1.951 × 2 Å) by covalent bonding with four nearest neighbor oxide ions. In CuO, the Cu-O distances of two more distant oxide ions to form a distorted octahedron are 2.784 Å (Åsbrink and Norrby, 1970). The coordination of copper group elements observed in halides, CuF2, CuCl2, K2CuF4, and AgF2 is referred to as 4 + 2 (Wells, 1962). Certain minerals with (Au,Ag)Te2 compositions also adopt a 4 + 2 coordination (Kitahara et al., 2022). However, in many cases Cu2+ has only one additional ligand at greater distances (i.e., a 4 + 1 coordination environment), which are regarded as tetragonal pyramidal coordination environments. Cu3(PO4)(OH)3 cornetite is a chemical analog of Cu3(AsO4)(OH)3 clinoclase. Cornetite and clinoclase are not isostructural. Cu is surrounded by five or six oxide and hydroxyl ions in a highly distorted polyhedral configuration. The polyhedral distortion of each Cu2+ site in cornetite has been interpreted as a typical Jahn-Teller effect by Eby and Hawthorne (1989). The distortion of Cu2+ sites from a regular octahedral coordination is sometimes explained as a consequence of the Jahn-Teller effect (Burns and Hawthorne, 1996), but an interpretation based on splitting of d orbitals from octahedral coordination is questionable. The Jahn-Teller theorem states that degenerate orbitals in a highly symmetric field are stabilized and lowered in energy by splitting the orbitals in a distorted environment with low symmetry. This theorem should not be applied to environments involving square planar covalent bonds or tetragonal pyramidal coordination. The Jahn-Teller effect focuses on the repulsion between the d orbital and the ligand, rather than considering the formation of covalent bonds. In clinoclase, callaghanite, and cornetite, the deviation from octahedral coordination is unusually large. The Cu-O distances within the square-base are approximately 1.96 Å. The Cu-O distances to the fifth neighbor are 12-27% longer than the average distances in the square-bases in clinoclase, calaghanite, and cornetite. The distortion of the coordination environment in these minerals should be interpreted in terms of covalent bonds that essentially form square planar coordination.
Bonding in transition metal oxides is described as more ionic rather than covalent. Cu is placed on the right side of the transition metals in the periodic table. The Cu-O and As-O bonds can be regarded as predominantly covalent from the difference in the Pauling’s electronegativity between Cu (1.90) or As (2.18) and oxygen (3.44). Four-coordinate Cu2+ ion can form square planar sp2d hybrid orbitals or distorted tetrahedral spd2 hybrid orbitals. Further, the five-coordinate Cu2+ can also form trigonal bipyramidal sp3d or spd3 hybrid orbitals and square pyramidal sp2d2, sd4, pd4 or p3d2 hybrid orbitals. Because Cu0 possesses ten 3d-electrons, confirming whether 4d orbitals are involved in bonding process is of notable scientific interest.
In this study, the crystal structures of clinoclase and callaghanite were investigated using single-crystal X-ray diffraction. An attempt was made to quantify and visualize the covalent bonding, anti-bonding, and net charge of each element using recent first-principle calculations. Nature of the hydrogen bonds was described based on hydrogen atom positions on the difference Fourier maps. We describe the contribution of hydrogen bonding and van der Waals bonding to the stabilization of sheet structure and large cavities in the structures. We discuss the complex structures and differences in feature of largely distorted Cu sites in clinoclase and callaghnite. The cause of the large dispersion of bond distances within the square base of Cu sites in clinoclase is also discussed based on the results of recent first-principles calculations.
EXPERIMENTS
Chemical composition, data collection, and crystal structure refinement
Single crystals of clinoclase and callaghnite were obtained from Ikuchishima, Setoda, Hiroshima, Japan (Sample No., Kumamoto University, C133-clinoclase-201202) and Sierra Magnesite Mine, Dabbs District Granite Canyon, Nevada, USA (Sample No., Kumamoto University, C133-callaghnite-201301), respectively. The chemical compositions were determined using a JEOL scanning electron microscope (SEM, JSM-7001F operated at 15 kV, 1.0 nA) equipped with an Oxford energy-dispersive X-ray spectrometer (EDS, INCA SYSTEM). The following standard materials were employed: MgO for Mg, pure Cu for Cu, and pure As for As. For clinoclase, the average of 11 analyses yielded 62.5(2) wt% of CuO and 30.1(4) wt% of As2O5, thereby providing a total of 92.6 wt%. Small amounts of Ca, Fe, and Si were detected as trace or contaminating elements, while no significant minor elements were detected. For callaghanite, the average of 8 analyses yielded 21.5(3) wt% of MgO and 42.7(3) wt% of CuO, thereby providing a total of 64.1 wt%. Trace amounts of Ca and Si were detected (less than 0.1wt%), and no other minor elements was observed. The empirical formula for the specimens were Cu3AsO4(OH)3 for clinoclase and Cu2Mg2(CO3)(OH)6·2H2O for callaghanite. The ideal chemical compositions of both minerals were used for structural refinements.
Single crystals were carefully selected and crystallographic data were collected on a XtaLAB Synergy, single source at offset/far, HyPix6000 diffractometer. Systematic absences were consistent with the space groups P21/c and C2/c. The intensities of reflections were measured using MoKα radiation (0.71073 Å). A total of 4573 and 4491 reflections were collected for clinoclase and callaghnite, respecively. Details of data correction method are described in each CIF file (Supplementary CIF files are available online from https://doi.org/10.2465/jmps.240925). Structure was refined using the SHELXL program (Sheldrick, 2015). The initial structures were solved using direct methods. The numbers of unique reflections were 1734 for clinoclase and 1057 for callaghnite. Difference Fourier calculations were utilized to determine the hydrogen atom positions in the structures. The R1 indices (R1 = Σ||Fo| − |Fc||/Σ|Fo|) converged to 0.0222 for clinoclase and 0.0368 for callaghnite using anisotropic displacement (Debye-Waller) parameters. The crystallographic data, atomic coordinates, displacement parameters and selected interatomic distances are listed in Tables 1-7. The crystal structures were illustrated using VESTA (Momma and Izumi, 2011).
Table 1. Crystallographic data, data collection parameters, and refinement parameters for clinoclase ad callaghanite
| |
Clinoclase |
Callaghanite |
| Chemical formula |
Cu3AsO4(OH)3 |
Cu2Mg2(CO3)(OH)6·2H2O |
| Temperature (K) |
293(2) |
| Space group |
P21/c (No.14) |
C2/c (No.15) |
| a (Å) |
7.2798(3) |
10.0168(9) |
| b (Å) |
6.4694(2) |
11.7671(10) |
| c (Å) |
12.4172(5) |
8.2383(6) |
| β (°) |
99.5060(10) |
107.416(6) |
| V (Å3) |
576.77(4) |
926.53(14) |
| Density (g/cm3) |
4.383 |
2.680 |
| Z |
4 |
| F(000) |
716 |
744 |
| Radiation type and wavelength (Å) |
MoKα, 0.71073 |
| μ (mm−1) |
86.426 |
4.777 |
| Crystal size (mm) |
0.015 × 0.032 × 0.095 |
0.072 × 0.089 × 0.078 |
| Diffractometer |
XtaLAB Synergy, Single source diffractometer
with an HyPix6000 area detector |
| 2θ range (°) |
≤61 |
≤61 |
| No. of measured reflections |
4573 |
4491 |
| No. of Independent reflections |
1734 |
1057 |
| Rint |
0.0245 |
0.0559 |
| R1 |
0.0222 |
0.0368 |
| wR2 |
0.0548 |
0.0612 |
| Goodness of fit, S |
1.343 |
1.023 |
| Lagest diff. peak/hole (e Å−3) |
0.942/−1.012 |
0.497/−0.578 |
Table 2. Atomic coordinates and equivalent atomic displacement parameters for clinoclase
| |
x |
y |
z |
Ueq or Uiso (Å2) |
| Cu1 |
0.78742(7) |
0.14005(7) |
0.32933(4) |
0.01073(14) |
| Cu2 |
0.81501(7) |
0.38128(7) |
0.12754(4) |
0.00985(14) |
| Cu3 |
0.38697(7) |
0.35302(7) |
0.41261(4) |
0.01140(14) |
| As |
0.30893(5) |
0.14980(6) |
0.17962(3) |
0.00748(12) |
| O1 |
0.4144(4) |
0.0719(5) |
0.0737(2) |
0.0118(5) |
| O2 |
0.1616(4) |
0.3436(4) |
0.1355(2) |
0.0116(5) |
| O3 |
0.1802(4) |
−0.0534(4) |
0.2131(2) |
0.0102(5) |
| O4 |
0.4707(4) |
0.2197(5) |
0.2854(2) |
0.0123(5) |
| O5 |
0.7795(5) |
0.2018(5) |
0.4778(2) |
0.0184(6) |
| O6 |
0.1937(4) |
0.5959(5) |
0.3232(2) |
0.0102(5) |
| O7 |
0.1810(4) |
0.1688(4) |
0.4094(2) |
0.0135(6) |
| H51 |
0.7675 |
0.3524 |
0.4923 |
0.028 |
| H61 |
0.0922 |
0.5424 |
0.3343 |
0.015 |
| H71 |
0.1559 |
0.1828 |
0.4793 |
0.020 |
Table 3. Anisotropic atomic displacement parameters (Å
2) for clinoclase
| |
U11 |
U22 |
U33 |
U23 |
U13 |
U12 |
| Cu1 |
0.0175(3) |
0.0083(2) |
0.0068(2) |
0.00027(16) |
0.00297(17) |
0.00138(16) |
| Cu2 |
0.0154(2) |
0.0074(2) |
0.0068(2) |
0.00017(16) |
0.00207(17) |
−0.00004(16) |
| Cu3 |
0.0150(3) |
0.0118(2) |
0.0081(2) |
−0.00267(16) |
0.00433(10) |
−0.00395(16) |
| As |
0.0096(2) |
0.00694(19) |
0.00602(19) |
−0.00038(12) |
0.00162(13) |
−0.00053(12) |
| O1 |
0.0113(12) |
0.0162(14) |
0.0087(11) |
0.0006(11) |
0.0036(10) |
0.0055(10) |
| O2 |
0.0143(13) |
0.0086(12) |
0.0119(12) |
0.0004(10) |
0.0020(11) |
0.0002(10) |
| O3 |
0.0123(12) |
0.0093(12) |
0.0091(11) |
−0.0008(10) |
0.0022(10) |
−0.0020(10) |
| O4 |
0.0105(12) |
0.0154(14) |
0.0106(11) |
−0.0060(11) |
0.0003(10) |
0.0002(10) |
| O5 |
0.0348(18) |
0.0151(14) |
0.0056(12) |
−0.0013(11) |
0.0041(12) |
0.0034(13) |
| O6 |
0.0117(12) |
0.0109(12) |
0.0085(11) |
0.0017(10) |
0.0028(10) |
−0.0002(10) |
| O7 |
0.0192(14) |
0.0097(12) |
0.0125(12) |
−0.0028(10) |
0.0055(11) |
−0.0043(10) |
Table 4. Selected bond distances (Å) and hydrogen bond geometry in clinoclase
| Cu1-O5 |
1.896(3) |
Cu2-O5 |
1.912(3) |
Cu3-O7 |
1.910(3) |
As-O4 |
1.675(3) |
| Cu1-O6 |
1.943(3) |
Cu2-O7 |
1.917(3) |
Cu3-O4 |
1.982(3) |
As-O2 |
1.682(3) |
| Cu1-O2 |
1.988(3) |
Cu2-O6 |
1.949(3) |
Cu3-O1 |
2.011(3) |
As-O1 |
1.705(3) |
| Cu1-O3 |
2.075(3) |
Cu2-O3 |
2.018(3) |
Cu3-O1 |
2.036(3) |
As-O3 |
1.706(3) |
| Cu1-O4 |
2.337(3) |
Cu2-O2 |
2.520(3) |
Cu3-O6 |
2.273(3) |
Cu3-Cu3 |
3.1404(5) |
| Cu1-O1 |
2.879(3) |
Cu2-O4 |
3.321(3) |
Cu3-O5 |
3.002(4) |
Cu1-Cu2 |
2.9867(7) |
| D-H …A |
d(D-H) |
d(H..A) |
$\measuredangle$D-H..A |
d(D..A) |
| O5-H51…O1 |
0.997(3) |
2.021(3) |
133.2(2) |
2.799(5) |
| …O6 |
|
2.286(3) |
108.09(2) |
2.774(4) |
| O6-H61…O3 |
0.848(3) |
2.068(3) |
153.7(2) |
2.853(4) |
| O7-H71…O2 |
0.920(3) |
1.941(3) |
163.5(2) |
2.825(4) |
Table 5. Atomic coordinates and equivalent atomic displacement parameters for callaghanite
| |
x |
y |
z |
Ueq or Uiso (Å2) |
| Cu |
0.04841(4) |
0.010818(3) |
0.45590(5) |
0.01089(11) |
| Mg |
0.15643(10) |
0.31539(9) |
0.327664(12) |
0.0103(2) |
| C |
0 |
0.5403(4) |
0.25 |
0.0121(8) |
| O1 |
0.1168(2) |
0.48564(19) |
0.2787(3) |
0.0170(5) |
| O2 |
0 |
0.6486(3) |
0.25 |
0.0179(7) |
| O3 |
0.0176(2) |
0.26492(18) |
0.0993(2) |
0.0115(4) |
| O4 |
0.011511(19) |
0.95123(19) |
0.4957(3) |
0.0135(4) |
| O5 |
0.2223(2) |
0.15283(18) |
0.4171(3) |
0.0113(4) |
| O6 |
0.3325(2) |
0.32726(19) |
0.2481(3) |
0.0160(5) |
| H31 |
0.0261 |
0.0292 |
0.9938 |
0.017 |
| H41 |
0.01992 |
0.9550 |
0.5762 |
0.020 |
| H51 |
0.2618 |
0.1000 |
0.3766 |
0.017 |
| H61 |
0.3773 |
0.2735 |
0.2534 |
0.024 |
| H62 |
0.3608 |
0.3590 |
0.1777 |
0.024 |
Table 6. Anisotropic atomic displacement parameters (Å
2) for callaghanite
| |
U11 |
U22 |
U33 |
U23 |
U13 |
U12 |
| Cu |
0.00982(16) |
0.00876(18) |
0.01414(18) |
0.00114(16) |
0.00364(13) |
−0.00082(14) |
| Mg |
0.0091(4) |
0.0085(5) |
0.0126(5) |
0.0007(4) |
0.0022(4) |
−0.0002(4) |
| C |
0.0152(19) |
0.008(2) |
0.0112(19) |
0.0 |
0.0015(17) |
0.0 |
| O1 |
0.0117(10) |
0.0113(12) |
0.0257(12) |
0.0016(9) |
0.0019(9) |
0.0033(8) |
| O2 |
0.0157(14) |
0.0090(16) |
0.0294(18) |
0.0 |
0.0076(14) |
0.0 |
| O3 |
0.0110(9) |
0.0111(11) |
0.0124(10) |
−0.0014(9) |
0.0035(8) |
−0.0009(8) |
| O4 |
0.0112(10) |
0.0117(11) |
0.0176(11) |
0.0010(9) |
0.0042(9) |
−0.0016(8) |
| O5 |
0.0116(9) |
0.0082(10) |
0.0146(10) |
0.0001(8) |
0.0048(8) |
0.0007(8) |
| O6 |
0.0150(10) |
0.0150(12) |
0.0208(11) |
0.0040(10) |
0.0095(9) |
0.0037(9) |
Table 7. Selected bond distances (Å), angles (°), and hydrogen bond geometry in callaghanite
| Cu-O4 |
1.9291(19) |
Mg-O1 |
2.059(2) |
C-O2 |
1.275(5) |
| Cu-O5 |
1.936(2) |
Mg-O3 |
2.064(2) |
C-O1 × 2 |
1.293(3) |
| Cu-O4 |
1.958(2) |
Mg-O6 |
2.062(2) |
|
|
| Cu-O3 |
1.966(2) |
Mg-O5 |
2.085(2) |
$\measuredangle$ O2-C-O1 × 2 |
119.8(2)° |
| Cu-O6 |
2.491(3) |
Mg-O3 |
2.094(2) |
$\measuredangle$ O1-C-O1 |
120.4(4)° |
| |
|
Mg-O5 |
2.123(2) |
|
|
| Cu-Mg |
2.9861(11) |
|
|
|
|
| Cu-Mg |
3.0943(10) |
Mg-Mg |
3.0095(19) |
|
|
| Cu-Cu |
2.8934(8) |
Mg-Mg |
3.280(2) |
|
|
| D-H…A |
d(D-H) |
d(H..A) |
$\measuredangle$D-H..A |
d(D..A) |
| O3-H31…O2 |
0.953(2) |
2.068(1) |
168.2(1) |
3.007(2) |
| O4-H41…O1 |
0.904(2) |
1.999(2) |
161.1(2) |
2.869(3) |
| O5-H51…O1 |
0.856(2) |
2.420(2) |
166.8(2) |
3.260(3) |
| O6-H61…O2 |
0.769(2) |
1.921(3) |
173.2(2) |
2.687(4) |
| O6-H62…O4 |
0.809(2) |
1.866(3) |
166.0(2) |
2.659(3) |
First principles calculations
Theoretical studies were performed to understand bonding characteristics of clinoclase and callaghanite based on a first-principles computational method (Shimojo et al., 2001) using QXMD code (Shimojo et al., 2019). Electronic states were calculated using the projector augmented-wave (PAW) method within the framework of density functional theory (DFT) (Blöchl, 1994). The generalized gradient approximation (GGA) functional proposed by Perdew et al. (1996) was employed to determine the exchange-correlation energy. The DFT-D method was employed for semiempirical correction of van der Waals interactions (Grimme et al., 2010). Momentum-space formalism was utilized, where the plane-wave cutoff energies were 30.0 and 250.0 Ry for the electronic pseudo-wave function and pseudo-charge density, respectively (Ihm et al., 1979). The energy was minimized with respect to the Kohn-Sham orbitals using a preconditioned conjugate-gradient method (Kresse and Furthmüller, 1996). Projector functions were generated for the 4s, 4p, and 4d states as the valence states for arsenic, for the 4s, 4p, and 3d states for cupper and 2s and 2p for oxygen atoms. The electron configuration of Cu2+ is [Ar] 4s03d9. No significant contribution from the 4d state was observed for Cu. Therefore, the calculations were performed up to 3d4s4p. Periodic boundary conditions were applied to all Cartesian directions. Structural optimizations of clinoclase and callaghnite were performed using experimentally determined crystallographic data of the monoclinic unit cell containing 56 and 104 atoms, respectively. Monkhorst-Pack grids of 2 × 2 × 2 k points were used for Brillouin zone sampling. We obtained the minimum-energy atomic configuration under 0.0 K and 0.0 GPa using the quasi-Newton method. The calculated lattice constants and atomic coordinates (Tables 8 and 9) are in good agreement with our refined structures. The atomic net charge of each atom and the bond overlap population of each pair of atoms (Tables 10 and 11) were calculated based on the population analysis method (Mulliken, 1955).
Table 8. Optimized atomic coordinates and difference (
Δ) between experimental and calculated values for clinoclase
| Calc. |
|
Δ |
|
|
|
|
| a |
7.2225 |
0.0573 |
|
|
|
|
| b |
6.4921 |
−0.0227 |
|
|
|
|
| c |
12.4393 |
−0.0221 |
|
|
|
|
| β |
100.4916 |
−0.9856 |
|
|
|
|
| |
x |
Δ |
y |
Δ |
z |
Δ |
| Cu1 |
0.7867 |
0.0008 |
0.1438 |
−0.0038 |
0.3297 |
−0.0004 |
| Cu2 |
0.8197 |
−0.0047 |
0.3753 |
0.0060 |
0.1259 |
0.0016 |
| Cu3 |
0.3731 |
0.0138 |
0.3559 |
−0.0028 |
0.4096 |
0.0030 |
| As |
0.3108 |
−0.0018 |
0.1486 |
0.0012 |
0.1800 |
−0.0004 |
| O1 |
0.4140 |
0.0005 |
0.0595 |
0.0124 |
0.0707 |
0.0030 |
| O2 |
0.1617 |
−0.0001 |
0.3481 |
−0.0045 |
0.1305 |
0.0050 |
| O3 |
0.1686 |
0.0116 |
−0.0548 |
0.0014 |
0.2141 |
−0.0010 |
| O4 |
0.4799 |
−0.0092 |
0.2150 |
0.0047 |
0.2898 |
−0.0044 |
| O5 |
0.7875 |
−0.0080 |
0.2014 |
0.0004 |
0.4788 |
−0.0010 |
| O6 |
0.1915 |
0.0022 |
0.5931 |
0.0028 |
0.3245 |
−0.0013 |
| O7 |
0.1809 |
0.0001 |
0.1580 |
0.0108 |
0.4132 |
−0.0038 |
| H51 |
0.7378 |
0.0297 |
0.3478 |
0.0046 |
0.4777 |
0.0146 |
| H61 |
0.0596 |
0.0326 |
0.5290 |
0.0134 |
0.3187 |
0.0156 |
| H71 |
0.1524 |
0.0035 |
0.1579 |
0.0249 |
0.4911 |
−0.0118 |
Table 9. Optimized atomic coordinates and difference (
Δ) between experimental and calculated values for callaghanite
| Calc. |
|
Δ |
|
|
|
|
| a |
9.9475 |
0.0693 |
|
|
|
|
| b |
11.8505 |
−0.0834 |
|
|
|
|
| c |
7.9933 |
0.2450 |
|
|
|
|
| β |
106.3700 |
1.0460 |
|
|
|
|
| |
x |
Δ |
y |
Δ |
z |
Δ |
| Cu |
0.0489 |
−0.0005 |
0.1127 |
−0.0046 |
0.4524 |
0.0035 |
| Mg |
0.1594 |
−0.0030 |
0.3146 |
0.0008 |
0.3237 |
0.0040 |
| C |
0.0000 |
0.0000 |
0.5418 |
−0.0014 |
0.2500 |
0.0000 |
| O1 |
0.1200 |
−0.0032 |
0.4878 |
−0.0022 |
0.2712 |
0.0075 |
| O2 |
0.0000 |
0.0000 |
0.6545 |
−0.0059 |
0.2500 |
0.0000 |
| O3 |
0.0153 |
0.0023 |
0.2678 |
−0.0029 |
1.0932 |
0.0061 |
| O4 |
0.1127 |
0.0024 |
0.9555 |
−0.0042 |
0.5035 |
−0.0078 |
| O5 |
0.2254 |
−0.0031 |
0.1504 |
0.0024 |
0.4152 |
0.0019 |
| O6 |
0.3338 |
−0.0013 |
0.3300 |
−0.0027 |
0.2403 |
0.0078 |
| H31 |
0.0242 |
0.0019 |
0.3004 |
−0.0084 |
0.9805 |
0.0133 |
| H41 |
0.2103 |
−0.0111 |
0.9553 |
−0.0003 |
0.5901 |
−0.0138 |
| H51 |
0.2674 |
−0.0056 |
0.0905 |
0.0096 |
0.3566 |
0.0201 |
| H61 |
0.3832 |
−0.0059 |
0.2549 |
0.0186 |
0.2350 |
0.0184 |
| H62 |
0.3552 |
0.0056 |
0.3836 |
−0.0246 |
0.1476 |
0.0301 |
Table 10. Mulliken’s population of electrons and contribution of each orbital and atomic net charge in clinoclase
| Clinoclase (DFT-D) |
| |
s |
p |
d |
Total |
Net charge |
| As |
1.186 |
1.796 |
0.811 |
3.793 |
1.207 |
| Cu1 |
0.397 |
0.363 |
9.643 |
10.404 |
0.596 |
| Cu2 |
0.455 |
0.375 |
9.582 |
10.412 |
0.588 |
| Cu3 |
0.394 |
0.391 |
9.668 |
10.453 |
0.547 |
| Cu (ave.) |
0.415 |
0.376 |
9.631 |
10.423 |
0.577 |
| O1 |
1.845 |
4.798 |
|
6.643 |
−0.643 |
| O2 |
1.858 |
4.804 |
|
6.662 |
−0.662 |
| O3 |
1.850 |
4.802 |
|
6.652 |
−0.652 |
| O4 |
1.861 |
4.780 |
|
6.641 |
−0.641 |
| O5 |
1.819 |
4.838 |
|
6.657 |
−0.657 |
| O6 |
1.822 |
4.810 |
|
6.632 |
−0.632 |
| O7 |
1.822 |
4.827 |
|
6.649 |
−0.649 |
| O (ave.) |
1.840 |
4.808 |
|
6.648 |
−0.648 |
| H51 |
0.470 |
|
|
0.470 |
0.53 |
| H61 |
0.468 |
|
|
0.468 |
0.532 |
| H71 |
0.466 |
|
|
0.466 |
0.534 |
| H (ave.) |
0.468 |
|
|
0.468 |
0.532 |
Projector functions were generated as the valence states for the 4s4p4d states for arsenic, 4s4p3d states for cupper, 2s2p state for oxygen, and 1s state for hydrogen atoms. The Cu (ave.), O (ave.), and H (ave.) rows show per-atom value of Mulliken’s population of electrons and net charge of Cu, O, and H, respectively.
Table 11. Mulliken’s population of electrons and contribution of each orbital and atomic net charge in callaghanite
| Callaghanite (DFT-D) |
| |
s |
p |
d |
Total |
Net charge |
| Cu |
0.466 |
0.489 |
9.702 |
10.658 |
0.342 |
| Mg |
0.257 |
0.424 |
0.406 |
1.087 |
0.913 |
| C |
0.941 |
2.518 |
|
3.458 |
0.542 |
| O1 |
1.779 |
4.784 |
|
6.563 |
−0.563 |
| O2 |
1.780 |
4.826 |
|
6.606 |
−0.606 |
| O3 |
1.796 |
4.921 |
|
6.717 |
−0.717 |
| O4 |
1.827 |
4.856 |
|
6.683 |
−0.683 |
| O5 |
1.798 |
4.911 |
|
6.708 |
−0.708 |
| O6 |
1.801 |
5.014 |
|
6.814 |
−0.814 |
| O (ave.) |
1.798 |
4.891 |
|
6.689 |
−0.682 |
| H31 |
0.537 |
|
|
0.537 |
0.463 |
| H41 |
0.556 |
|
|
0.556 |
0.444 |
| H51 |
0.551 |
|
|
0.551 |
0.449 |
| H61 |
0.562 |
|
|
0.562 |
0.438 |
| H62 |
0.532 |
|
|
0.532 |
0.468 |
| H (ave.) |
0.548 |
|
|
0.548 |
0.452 |
Projector functions were generated as the valence states for the 4s4p3d states for cupper, 3s3p3d states for magnesium, 2s2p state for oxygen, and 1s state for hydrogen atoms. The O (ave.) and H (ave.) rows show per-atom value of Mulliken’s population of electrons and net charge of O and H, respectively.
RESULTS AND DISCUSSION
Description of the crystal structure of clinoclase
Figures 1 and 2 show the crystal structure of clinoclase. Selected interatomic distances are presented in Table 4. The As5+ ion is located at a general position and is tetrahedrally surrounded by four oxide ions (O1, O2, O3, and O4). The four As-O distances are divided into two groups of 1.68 and 1.71 Å. As-O1 and As-O3 distances were characteristically elongated. Cu3-O1 and Cu1-O3 bonds are in equatorial square bases and O1 and O3 are oxide ions that form shared edges between Cu polyhedra. When the electrostatic contribution of Cu to O1 and O3 is large, the contribution of As becomes small and the As-O distances are elongated. O2 and O4 play the role of shared corners among polyhedra. Each O2 and O4 is bonded to one As and two Cu atoms. One of the two Cu-O distances [Cu2-O2 = 2.520(3) and Cu1-O4 = 2.337(3) Å] is significantly longer than the distances in equatorial square bases, resulting in smaller electrostatic contributions of Cu2 and Cu1 and larger contributions of As to O2 and O4. The As-O2 and As-O4 distances become shorter due to the large electrostatic contribution of As. All oxygen atoms other than O1 to O4 belong to hydroxyl groups.
Figure 1. Crystal structure of clinoclase. Thermal ellipsoids are drawn at 90% probability level. (a) The Cu1Cu2(OH)4O4 and Cu32(OH)4O4 dimers, along with As tetrahedra, share vertices to form a complex sheet structure parallel to the (100) plane. (b) These sheets are interconnected through long Cu2-O2 and Cu1-O7 van der Waals bonds, as well as O6-H61…O3 hydrogen bonds.
Figure 2. Intralayer hydrogen bonds in clinoclase. Thermal ellipsoids are drawn at 90% probability level. O5, which bonds to Cu1, Cu2, and H51, exhibits significant thermal vibration amplitude perpendicular to the Cu-O-Cu bond.
There are three crystallographically independent Cu2+ sites with different coordination environments in clinoclase structure. The fifth neighbour Cu2-O2 at 2.524(3) Å is not included in the coordination of the Cu2 site and Cu2 has a distorted square planar (4 + 0) four-coordination environment (Eby and Hawthorne, 1990). Cu1 and Cu3 occupy tetragonal pyramidal (4 + 1) five-coordination sites with large distortion.
The Cu1 atom is surrounded by two hydroxyl and two oxide ions in an equatorial square base with Cu-O distances of 1.896(3), 1.943(3), 1.988(3), and 2.075(3) Å. The fifth nearest anion, O4, is located at 2.337(3) Å apart, and the sixth nearest anion, O1 is 2.879(3) Å apart. The diagonal angle in the -O3-O5-O2-O6- square base is $\measuredangle$O2-Cu1-O3 = 162.29(13)° and $\measuredangle$O5-Cu1-O6 = 175.67(15)°. Coordination polyhedron is closer to a tetragonal pyramid than a trigonal bipyramid (the O-Cu-O angle of the equatorial triangular plane is 120°). The coordination environment of Cu2 is distorted square (rectangle) planar. Three hydroxyl and one oxide ions surround Cu2 in a square base with Cu-O distances of 1.912(3), 1.917(3), 1.949(3), and 2.018 Å. The fifth and sixth nearest anions, O2 and O4, are 2.524(3) and 3.321(3) Å apart from Cu2, respectively. The diagonal angle in the -O3-O6-O5-O7- square base is $\measuredangle$O3-Cu2-O5 = 172.01(15)° and $\measuredangle$O6-Cu2-O7 = 172.01(15)°, fairly close to the ideal value. The tetragonal pyramidal Cu3 site has a distorted square base with one hydroxyl and three oxide ions with Cu-O distances of 1.910(3), 1.982(3), 2.011(3), and 2.036(3) Å. The fifth and sixth nearest anions are 2.273(3) and 3.002(4) Å apart from Cu3, respectively. The diagonal angle in the -O1-O1-O4-O7- square base is $\measuredangle$O1-Cu3-O4 = 153.33(13)° and $\measuredangle$O1-Cu3-O7 = 172.70(14)°. One only deviated approximately 7° from a straight line, while the other was between 180° and 120°.
In the square base, the average Cu-O distance is 1.976 Å for Cu1 site, 1.949 Å for Cu2 site, and 1.985 Å for Cu3 site. The differences between the shortest and longest distances (Δdistance) in square base are 0.179 Å for Cu1 site, 0.106 Å for Cu2 site, and 0.126 Å for Cu3 site. The values of Δdistance are as much as 9% of the average Cu-O distance. The bonding distances between Cu and O of hydroxyl ion were shorter than those between Cu and oxide ion.
Two sets of dimeric groups, Cu1Cu2(OH)4O4 and Cu32(OH)4O4, are formed by sharing one edge of the equatorial square base of the Cu coordination polyhedron. The Cu1 and Cu2 sites share an edge [O3-O6 = 2.637(3) Å] and the Cu1-Cu2 distance is 2.9869(4) Å. The Cu3 sites share an edge [O1-O1 = 2.541(3) Å] with each other to form a Cu2(OH)4O4 dimer. Shared edges are much shorter than unshared edges. The Cu3-Cu3 distance is 3.1404(5) Å. The Cu1-Cu2 distance [2.9867(7) Å] is shorter than the Cu3-Cu3 distance.
Structural relaxation due to electrostatic repulsion between cations was observed. The shared O3-O6 [2.637(3) Å] and O1-O1 [2.541(3) Å] edge distances of the Cu polyhera are shortened to enhance the shielding effect (Pauling, 1960). Some Cu-O distances [e.g., Cu1-O3 = 2.0700(14), Cu2-O3 = 2.0200(16), Cu3-O1 = 2.0365(17) and 2.003(3) Å] are elongated within the square base for the cation-cation repulsion (Pauling, 1960). The Cu position shifts to the opposite side of the shared edge for electrostatic repulsion between Cu atoms. In other words, an electrostatic interaction between Cu and Cu separated by about 3 Å is still apparent.
The Cu1Cu2(OH)4O4 and Cu32(OH)4O4 dimers share corners through oxide ions and hydroxyl groups. These dimers share corner with the As tetrahedron and they form a complex sheet structure (Eby and Hawthorne, 1990) parallel to the (100) plane (Fig. 1). There were three types of hydrogen bonds (O5-H51…O1, O5-H51…O6, and O7-H71…O2) within the sheet (Table 4 and Fig. 2). These sheets are held to each other through long Cu-O bonds [Cu2-O2 = 2.524(3) and Cu1-O7 = 2.877(2) Å] and O6-H61…O3 bonds [O6-O3 = 2.852(3) Å]. The long Cu2-O2 and Cu1-O7 bonds are assumed to have dominant ionic or van der Waals bond characters (Fig. 1). These distances are less than sum of van der Waals radius (2.92 Å) and longer than the sum of the ionic radii (VICu-IIIO = 2.09 Å, IVCu-IIIO = 1.93 Å, Shannon, 1976).
Table 3 lists the anisotropic atomic displacement parameters of clinoclase. Thermal vibrations of many atoms are characterized by large U11 value. All Cu atoms exhibit a large anisotropy in thermal vibration, the largest component of vibration was approximately perpendicular to the square base due to strong covalent bonding in the basal plane. Two different Cu1Cu2(OH)4O4 dimers are connected by sharing of the O5 corner (Fig. 2). O5 of the hydroxyl group is bonded only to two Cu atoms (Cu1 and Cu2) in addition to H. The hydroxyl group O5 has almost no structural restriction perpendicular to the Cu1-O-Cu2 bond and has the extremely large amplitude of thermal vibration perpendicular to the Cu1-O-Cu2 bonds.
Description of the crystal structure of callaghanite
Figures 3 and 4 show the crystal structure of callaghanite. Selected interatomic distances are listed in Table 7. The structure consisted of tetragonal pyramidal Cu sites, octahedral Mg sites and triangular carbonate ions. Carbonate ion are formed from C, O1, and O2 atoms. O3, O4, and O5 are hydroxyl groups and O6 is the oxide ion of water molecule. The O1 oxide ion has two strong bonds with C and Mg and is the acceptor ion for H41. The O2 oxide ion bound strongly only to C and was acceptor ion for two H31 and two H61. The hydroxyl groups O3 and O5 are strongly bonded to two Mg and one Cu and are donor ions for H31 and H51, respectively. The hydroxyl group O4 is bonded to two Cu atoms, and is a donor ion for H41 and an acceptor ion for H62. O6 of the water molecule bonds with Mg and Cu, and also a donor ion for H61 and H62.
Figure 3. Crystal structure of callaghanite. (a) The structure comprises tetragonal pyramidal Cu sites, octahedral Mg sites and triangular carbonate ions. A three-dimensional framework is formed by the edge-sharing of the Cu2(OH)6·2H2O units and the zigzag chains of Mg octahedra. (b) Tunnels are formed by extension of cavities along the [110] direction within the three-dimensional framework (highlighted in green ovals).
Figure 4. Interatomic distances involved in the distorted Cu tetragonal pyramid and MgO6 octahedron. The brown ellipses represent Mg atoms. Structural relaxation is observed owing to edge-sharing between adjacent polyhedra.
Cu2+ occupies a tetragonal pyramidal site with four hydroxide ions as the square base (-O3-O5-O4-O4-). The average Cu-O distance in the base is 1.947 Å. The difference, Δdistance, between the shortest [Cu-O4 = 1.9291(19) Å] and longest distances [Cu-O3 = 1.966(2) Å] in square base is 0.037 Å. The difference was only 2% of the average distance in callaghanite, which is one-fifth to one-third of the values observed in clinoclase. The water molecule (O6) is located at the apex of the pyramid with a long distance [2.491(3) Å] as the fifth ligand. The sixth ligand was not found. In callaghanite, Cu is not bound to the O1 and O2 oxide ions that form carbonate ions. The carbonate groups were not bonded to Cu ions. The diagonal angles in the -O3-O5-O4-O4- square base are $\measuredangle$O3-Cu-O4 = 176.24(12)° and $\measuredangle$O4-Cu-O5 = 173.90(12)°. The deviation from linearity or planarity was <6.1° and coordination polyhedron is a tetragonal pyramid. Cu is located at the center of the square base of the tetragonal pyramid.
The Cu2(OH)6·2H2O dimer is formed by sharing the O4-O4 edge of tetragonal pyramid with another tetragonal pyramid. There is a center of symmetry on the O4-O4 shared edge. Each O3-O5 and O5-O6 edge of the tetragonal pyramid is shared by two neighboring Mg octahedra. The shortest Cu-Cu distance is 2.8935(6) Å. Two different Cu-Mg distances across the shared edge are 2.9861(11) and 3.0942(9) Å. Structural relaxation due to repulsion between cations was observed. The O4-O4 [2.596(3) Å] of the shared edge between Cu and Cu is shortened to enhance the shielding effect (Pauling, 1960). On the other hand, the shortening of the O3-O5 [2.709(3) Å] and O5-O6 [2.978(3) Å] shared edges among Cu- and Mg-ployhedra is not significant.
Mg2+ is coordinated by one carbonate ion (O1), water molecule (O6) and four hydroxyl ions (O3, O3, O5, and O5). The Mg octahedra shared two edges with two adjacent Mg octahedra, forming a zigzag chain parallel to the [101] direction (Brunton et al., 1958). The Mg octahedron also shares two more edges with tetragonal Cu pyramids. A three-dimensional framework is constructed by sharing edges among polyhedral in the zigzag chains of Mg octahedra and the Cu2(OH)6·2H2O units. Carbonate ions connect the corners of the two Mg octahedra (Figs. 3 and 4).
The Mg-Cu distance across the shared O3-O5 edge [2.709(3) Å] is 2.9861(11) Å. The Mg-Cu distance across the shared O5-O6 edge [2.978(3) Å] is 3.0942(9) Å. The Mg-Mg distance across the shared O3-O3 edge [2.6103(19) Å] is 3.0096(12) Å. The Mg-Mg distance across the shared O5-O5 edge [2.636(4) Å] is 3.2803(13) Å. The electrostatic repulsion among cations is also moderated by the change in Mg-O distances within the Mg octahedron (Fig. 4). The variety of edge sharing manners and chemical species of ligand led to large variations in the Mg-O distances in the octahedron. Some Mg-O distances are elongated due to the electrical repulsion between cations (Fig. 4). The O1 oxide ion, which strongly binds only to C and Mg, has a short Mg-O distance [2.059(2) Å] due to the relatively large contribution of Mg to the bond valence sum. The difference between the shortest distance [Mg-O1 = 2.059(2) Å] and the longest distance [Mg-O5 = 2.123(2) Å], Δdistance, is 0.064 Å. The value of Δdistance is larger than that in the square base of the Cu tetragonal pyramid (Δdistance = 0.037 Å).
Cavities with carbonate ions and water molecules in callaghanite
Tunnels of cavities extending in the [110] direction are formed within a three-dimensional framework consisting of Mg octahedral zigzag chains and Cu2(OH)6·2H2O dimers (Fig. 3b). Water molecules and carbonate ions locate near the tunnels. H31, H61, and H62 atoms exist in the tunnels and hydrogen bonds are formed. The hydrogen atoms are continuously arranged in the [110] direction. A unique feature of this structure is that the O2 corner of the carbonate ion protrudes into the tunnel. Two types of oxide ions (O1, O2) are bound to C. The O2 that forms the carbonate group is bound to neither Mg nor Cu, but strongly bonded only to C. The C-O2 distance [1.274(6) Å] is shorter than that of C-O1 [1.293(4) Å] because O2 has a large electrostatic contribution (bond valence) with C. In contrast, the $\measuredangle$O1-C-O1 [120.4(3)°] and $\measuredangle$O1-C-O2 [119.8(3)°] angles are close to the ideal value. O2 was also the acceptor oxide for two H61 of water molecule and two H31 of hydroxide. This position of O2 is held in the tunnel only by four weak hydrogen bonds, in addition to a strong covalent bond with C. The C and O2 sites were located at the Wyckoff position 4e, with a site symmetry 2. Twofold rotation axis passes through C and O2. Triangular plane were arranged almost parallel to the (001) plane (tilted approximately 11° with respect to the plane). The local environment around C and O2 increased the amplitude and anisotropy of thermal vibrations of atoms associated with carbonate ions and water molecules near the cavities (Table 7 and Fig. 4). The anisotropic thermal vibrations of O2 and O1 were larger along <001>, which was perpendicular to the triangular carbonate plane. However, the anisotropic thermal vibration of C was larger in <100>, which was the in-plane direction of the triangular faces. Notably, the amplitude of U11 for C was the same as that for O2.
Chemical bonding properties and Cu2+-O distances in tetragonal pyramidal coordination
The chemical composition of clinoclase is simpler than that of callaghanite with various anions such as carbonate ion, hydroxide ion, and water molecule. However, the Cu square bases of tetragonal pyramid in clinoclase exhibit large variations in bond distances and are highly distorted. In callaghanite, the variation in bonding distances in the covalent Cu square base was small compared to that in the ionic Mg octahedron. There must be a relationship between the distortion of the Cu2+ polyhedral site and the relaxation of the electronic structure of the Cu2+ ions.
Figure 5 shows the variations in Cu-O distances in Cu tetragonal pyramidal sites in some minerals for which single crystal structure analyses have been performed. The Cu-O distances in the square planar coordination sites of CuO tenorite and the shorter cation-cation distance in each structure were also plotted for comparison. The variation in bonding distances within the square base differs between clinoclase and callaghanite, with each group having a similar variation. The average Cu-O distance within the square base is constant at approximately 1.96 Å, regardless of whether Cu has 5 or 6 neighboring oxygen atoms (Fig. 5). The fifth Cu-O distance varies from 2.142 to 2.491 Å, and the sixth from 2.387 to 3.002 Å. From the distribution of Cu-O distances, it can be interpreted that the coordination environment of Cu2+ in these minerals was essentially square planar dominated by covalent bonds. In addition to the four nearest neighbor coordination with mainly covalent bonding, Cu2+ has electrostatic interactions (rich in ionic or van der Waals bonding) with the oxide ion as the fifth or sixth weaker binding ligand.
Figure 5. Variations in Cu-O distances in Cu tetragonal pyramidal coordination sites across various minerals, including CuO tenorite. The oxygen coordination around Cu is best described as square planar, with one or two additional bonds involving weaker electrostatic interactions (either ionic or van der Waals bonds). The shorter Cu2+-O bonds in these minerals form square-planar covalent bonds (highlighted in red). The longer, additional fifth and sixth ligands are bound bythrough electrostatic interactions, such as ionic (highlighted in yellow) or van der Waals bonds (highlighted in grey). The sum of the van der Waals radii for Cu and O is 2.92 Å. Significant electrostatic interaction is observed up to 3 Å, with cation-cation (M-M) repulsion acting as a relaxation mechanism. A clear difference is observed in the variation of covalent Cu-O distances within the square base of the tetragonal pyramidal coordination. Two groups were identified: those with large variations (the clinoc-group, including clinoclase) and those with small variations (the callag-group, including callaghanite). The Cu2+ species in square planer coordination surrounded by both hydroxyl ions and oxide bonded to Group 15 elements exhibits significant variation in terms of Cu-O distances.
Cu-bearing compounds having topologically similar structures to the subjected compounds are divided into two groups: those with large variations (the clinoc-group, including clinoclase) and those with small variations (the callag-group, including callaghanite) in Figure 5. The difference between the longest and shortest Cu-O distances (Δdistance) within the square base is less than 0.041 Å for the callag-group. The difference (Δdistance) is as much as 0.179 Å in the clinoc-group. The clinoc-group includes [Cu3AsO4(OH)3] clinoclase, Cu2AsO4(OH) olivenite (Li et al., 2008), Cu3PO4(OH)3 cornetite (Eby and Hawthorne, 1989), and BiCu6(OH)6(AsO4)3·3H2O mixite (Miletich et al., 1997). The square bases of Cu2+ site in these minerals are composed of both hydroxyl groups and oxide ions. In this group, degree of variability in Cu-O distances within square base depends on the chemical species of the ligands. The square base of Cu2+ site, composed of both oxide and hydroxyl ions, exhibited large variations in the Cu-O distance. In the Cu ligands, certain oxide ions bonded to As or P cause changes in the covalent character of the Cu-O bond. In the Cu-O-M configuration, if the M-O bond is strong, the position of the oxide ion will be attracted from Cu towards M.
The callag-group includes [Cu2Mg2CO3(OH)6·2H2O] callaghanite, CuTeO3·2(H2O) teineite (Effenberger, 1977), Ca2Cu2Si3O10·2H2O kinoite (Laughon, 1971), and KNaCuSi4O10 litidionite (Pozas et al., 1975). The square base of Cu sites in callaghanite and litidionite are confined to hydroxide and oxide ions, respectively. The square-based Cu2+ site in teineite and kinoite are formed by both oxide ions and water molecules. The distances within the squares between Cu and oxide ion in teineite and kinoite tend to be slightly longer than those between Cu and the water molecule. However, the difference in the Cu-O distances within the square base between oxide ions and water molecules or between oxide ions and hydroxyl groups did not appear clearly. It is unlikely that a water molecule and hydroxyl group would have significantly different characteristics when forming a covalent bond with Cu2+. The difference between the clinoc- and callag-groups is not due to water molecules or hydroxyl groups.
Structural optimization by simulation and electronic structure in clinoclase and callaghanite
The experimentally determined unit cell constants and atomic coordinates of clinoclase and callaghanite were optimized via simulation. The calculated lattice constants and atomic coordinates are listed in Tables 8 and 9. The differences before and after optimization for each parameter were less than two percent. Regarding the coordinates of the H atoms, our observations represent the center of electron density distributions, whereas the simulations represent the nuclear positions; therefore, there are discrepancies between these values.
The coordinates of H atoms in clinoclase have been proposed using theoretical methods by Krivovichev (2017). Table 12 shows the distances (Å) and angles (°) derived from the simulated values for hydrogen bond geometry in clinoclase, where our results are compared with those of Krivovichev (2017). The overall trends are in good agreement. The donor oxygen-hydrogen distances we obtained are 0.05 Å longer, while the acceptor oxygen-hydrogen distances are more than 0.12 Å shorter than those by Krivovichev (2017). Note that the simulation setup conditions are different for the two models. All atomic positions and unit cell parameters were optimized in our simulation, but the effect of temperature was not taken into account. In the simulation by Krivovichev (2017), the atomic coordinates and unit cell parameters other than H were taken from experimental values at room temperature.
Table 12. Comparison of bond distances (Å) and angles (°) derived from the simulated values for hydrogen bond geometry in clinoclase
| D-H …A |
d(D-H) |
d(H..A) |
$\measuredangle$D-H..A |
d(D..A) |
Reference |
| O5-H51…O1 |
1.015 |
1.793 |
156.28 |
2.752 |
This study |
| |
0.965 |
1.912 |
148.87 |
2.783 |
Krivovichev (2017) |
| O6-H61…O3 |
1.030 |
1.713 |
169.29 |
2.732 |
This study |
| |
0.980 |
1.863 |
165.11 |
2.821 |
Krivovichev (2017) |
| O7-H71…O2 |
1.027 |
1.724 |
166.38 |
2.732 |
This study |
| |
0.979 |
1.846 |
164.17 |
2.801 |
Krivovichev (2017) |
The atomic net charge and contributions of each orbital to atomic charge of Cu and O in clinoclase and callaghanite are summarized in Tables 10 and 11. The ideal electron configuration for Cu2+ is [Ar] 4s03d9. The electron configuration of O2− is [He] 2s2 2p6. In clinoclase, the average total charges of 10.423 for Cu2+ and 6.648 for O2− changed from fully ionic by +1.423 and −1.352, respectively. The deviation from the fully ionic state indicates covalent nature (polarization) formed by electron sharing between the oxide ion and cation. The s-, p-, and d-orbitals contribute to covalent bonds of Cu2+. An average charge of approximately 0.36 is distributed within each orbital in the spd2-like covalent bond. A similar electronic state for Cu2+ was optimized in callaghanite, with an average charge of approximately 0.41 distributed within each orbital for Cu2+. The number of shared electrons in Cu-O bonds appeared to be higher for callaghanite than for clinoclase. This is related to the contribution of coexisting cationic species and the regularity of distances within the square planar coordination. In Table 10, the charge distribution of Cu is, contrary to expectations, closer to the spd2 hybrid orbital than the sp2d hybrid orbital, and the distribution of As is closer to the sp2d hybrid orbital.
Three-dimensional representations of covalent bonding (strong bonding) and anti-bonding around Cu atoms in clinoclase and callaghanite are shown in Figures 6 and 7, respectively. Equatorial square bases and the fifth oxide ion at a longer distance perpendicular to the base are indicated. No shared electrons were observed between the Cu2 and the fifth neighbor oxide ion (O2) in clinoclase. Each value represents the bond overlap population, and a higher value corresponds to a stronger bond. For callaghanite, the values of bond overlap population in the equatorial square bases were not widely dispersed and ranging from 0.37 to 0.29. The value between Cu and the fifth neighbor was approximately one-third (0.13) of that in square base. For clinoclase, the values in the square base varied widely, from 0.44 to 0.16. The values between Cu and hydroxyl groups are 0.44 to 0.35, while the values between Cu and oxide ions bound to arsenic are half of those values (0.22 to 0.17). Because of the electron sharing (covalent bond) between As and oxide ion, the bond between Cu and oxide ion bound to As is weaker compared to the Cu-OH bond.
Figure 6. Three-dimensional representation of bonding and anti-bonding interactions around the Cu atoms in clinoclase. The blue, green, and white spheres represent Cu, As, and H, respectively.
Figure 7. Three-dimensional representation of bonding and anti-bonding interactiona around the Cu atom in callaghanite. The blue and white spheres represent Cu and H, respectively.
In Figures 6 and 7, absolute values of partial orbital-orbital correlations for anti-bonding between As and Cu in clinoclase (−0.22 to −0.11) are larger than those between Cu and Cu or Mg in callaghanite (−0.14 to −0.11). Arsenic, which is adjacent to Cu via oxide ions, significantly affects the antibonding and covalent bonding of Cu. In Figure 5, the clinoc-group shows a wider dispersion of the covalent bond distances within the square base than the callag-group. The clinoc-group included the Group 15 elements, As and P. We conclude that the wide dispersion of distance within square planar covalent bonds in Cu compound minerals of clinoc-group can be attributed to the effects of adjacent highly covalent cations via oxide ion. Another highly covalent cation in the vicinity appears to significantly disrupt the Cu-O covalent state. The large distortion of the square planar coordination environment of Cu was caused by the chemical bonds between the oxide ions and As and by the repulsion between orbitals of Cu and As. The coordination environment around a highly covalent element is disrupted by adjacent highly covalent atoms. The Δdistance of the AsO4 tetrahedron in clinoclase structure is 0.03 Å. The electronegativity of Si is the same as that of Cu. The SiO4 tetrahedra in kinoite and litidionite structures (Laughon, 1971; Pozas et al., 1975) have a very large distortion with Δdistance = 0.06 Å. The effect of the covalent bonding of Cu to Si will be reported in detail in another paper.
