Natural arsenic with a unique order structure: potential for new quantum materials
Natural arsenic with a unique order structure: potential for new quantum materials
Makoto t okuda
study of arsenic (As) provides guidelines for the development of next-generation materials. We clarify the unique structure of the third crystalline polymorph of natural As (Pnm21-As) by crystallographical experiment and the electronic structure by first-principles computational method. The crystal structure of Pnm21-As is a novel structure in which the basic portions of semi-metalic grey-As and semi-conductor black-As are alternately arranged at the atomic level. For both covalent and van der Waals bonding, the contributions of sd and pd hybridizations are important. Van der Waals bonding characteristics and d orbital contributions can be varied by control of layer stacking. t otal charges are clearly divided into positive and negative in the same elements for the grey-As and black-As portions, respectively, is of importance. the sequence in which one-dimensional electron donor and acceptor portions alternate in the layer will be the first description.
Crystalline polymorph of arsenic. A third crystalline polymorph of natural arsenic was discovered in
Japan and named pararsenolamprite1. Pararsenolamprite is more resistant to alteration by weathering or
oxidation than grey arsenic (R3 m-As). The possibility for two space groups (Pnm21 is one of the proposed) was pointed
out1 and the crystal structure was not determined. Determination of the unknown structure requires
measurement of a wide range of diffraction peak intensities. Here, we clarify the unique structure of this third crystalline
mineral phase of arsenic (pararsenolamprite) by superior experimental equipment and its electronic structure by
simulation and discuss its possibility in the creation of new functional materials. Pararsenolamprite holds
precisely the intermediate structure in which structural R3 m-As and Bmab-As are regularly arranged.
Electric properties of semiconductor to metal in group-V elements have been extensively studied in the fields
of physics, chemistry and materials sciences1?6. The series P, As and Sb in group V elements shows a gradation
of properties from non-metal to metal. Several phases in P, As and Sb have superconducting properties7?9. The
physical properties in group-V elements are highly anisotropic due to asymmetric chemical bonding
character. Non-simple structures are described as follows: covalently bonded atomic layers are weakly held together
by van der Waals? force, can easily cleave in the corresponding plane, and design a two-dimensional structure.
Two-dimensional semiconductors have been proposed due to their promising device characteristics such as black
phosphorus consisting of layer of phoshorene10. The study of single element materials such as P and As will give
guidelines for the development of next-generation materials.
Single element arsenic minerals are well known for two polymorphs of crystalline phases named arsenic
(space group R3 m) and arsenolamprite (space group Bmab). Semi-metallic grey arsenic (R3 m-As) is the most
common and is believed to be the stable form of arsenic under ambient conditions. It is crystallized in a
rhombohedral structure with space group R3 m (A7-type structure). Black arsenic (black to dark-grey, Bmab-As) is glassy
crystal and is isostructure with black phosphorous11?13. It can be prepared by cooling arsenic vapor at 100?220 ?C
or by heating amorphous As at 100?175 ?C in the presence of Hg14. Black arsenic converts to semi-metallic grey
arsenic at around 520 K. It is reported from theoretical calculations that pure black-arsenic is metastable and is
stabilized by impurities15. The metastable yellow insulator arsenic consists of As4 molecules and has the same
configuration as the P4 molecule. This allotrope is prepared by condensing the vapour on glass substrates at a very
low temperature. This form is destroyed by X-ray radiation and transforms to semi-metallic grey arsenic at
temperature above 30 K. No P-T phase diagram with crystalline forms has been proposed in the arsenic system16.
Arsenic has five valence electrons. Fundamentally, the number of bonds for covalent substances is 8-N,
where N is the ordinal number of the Periodic Group, e.g. 8-5 = 3 for As. Each atom in arsenic polymorphs is
in three-fold coordination as expected for the covalent bonding with electronic configuration s2p3. The s-orbital
is fully occupied with two electrons and does not contribute to cohesion. The cohesion is dominated by the
half-filled p orbitals. The group-V element As in its crystalline structure can be simply explained as the results of
Peierls distortion of p-bonded atoms. The six lobes of the p orbitals lead to a simple cubic structure. Simple cubic
to A7 distortion removes p orbital degeneracy and results in the formation of three saturated nearest-neighbor
bonds. Doubling of the periodicity in the three principal directions of the simple cubic structure can be achieved
by the alternation of short covalent bonds and long van der Waals bonds. This leads to a layer structure of
tri-coordinated covalent atoms. The reason group V elements are semiconductors or semimetals is due to a gap
at the Fermi level opened by the doubling of periodicity. The electron configuration of As is 4s2 3d10 4p3, in which
there are d orbitals in addition to s and p orbitals. Clarifying the contribution of d orbitals is important for
understanding physical properties and subsequent material design.
Crystal structure, morphology, twinning and comparison with other As phases. The crystal
structure of Pnm21-type As was determined by single crystal X-ray diffraction method using superior
experimental equipment. Since good single crystals could be found out and a good diffraction data set was obtained, the
structure could be determined by the direct method (details are in the CIF file). The crystals are naturally
occurring arsenic containing three percent antimony element of the homologous elements. Figure?1a,b show the crystal
structure projected on (010) and (001), respectively. There are eight kinds of crystallographically non-equivalent
As sites (Extended Data Table?1). All atoms are on the mirror plane parallel to (010). The As sites repeat as
-As1-As2-As2?-As1?-As3?-As4?-As4-As3-As1- along a axis, or in opposite direction. The three-connected
(buckled) six-gon layer bends at the As4?-As4 or As4-As4? positions. Structurally, eight kinds of crystallographically
equivalent As sites are divided into four pairs, As1-As1?, As2-As2?, As3-As3? and As4-As4?. This structure can also
be divided into two portions like As1-As2-As2?-As1? (yellowish green sphere in Fig.?1a) and As3?-As4?-As4-As3
Figure?1b shows a comparison of crystal structures among the crystalline arsenic phases (Pnm21-As
(pararsenolamprite), R3 m-As (semi-metallic grey native arsenic) and Bmab-As (black arsenic, arsenolampite)). It was
revealed that the structure of Pnm21-As, pararsenolamprite, is a mixed structure in which the structural units of
grey- and black-As are regularly arranged. The structure of Pnm21-As consists of 1:1 packing of R3 m-As and
Bmab-As basic units. The array represents as a herringbone pattern consisting of two units.
The short covalent bond distances and angles in Pnm21-As are presented in Extended Data Table?2. Bonding
distances and angles are useful indicators of chemical bonding properties and orbitals of bonding electrons and
allow comparisons among crystalline polymorphs. As with four pair positions can be divided into two groups
with average bond angles greater (As3 (98.2?) and As4 (96.3?)) or smaller (As1? (89.4?) and As2 (94.0?)) than the
average value of 94.45?. The intralayer and interlayer As-As distances in Pnm21-type As are intermediate between
R3 m-type and Bmab-type As and have a spread in value.
The determined relationship between crystal morphology and unit cell axis for Pnm21-As is shown in Fig.?2.
A twin boundary and striations on the crystal surface are observed parallel to the b-axis. The structure of
Pnm21-As consists of a packing of R3 m- and Bmab-As portions (Fig.?1b). Both portions are parallel to the b-axis,
and twinning and striations occur due to the change in the periodicity of the portions. A certain twin crystal will
change the ratio of each R3 m- and Bmab-As portion.
structural optimization by simulation and electronic structure in Pnm2 1-As. Experimentally
determined unit cell constants, cell volume and atomic coordinates for Pnm21-As were well optimized by the
simulation. Differences between before and after optimization for each parameter were one percent or less.
Covalent bonding (strong bonding), van der Waals bonding (weak bonding), and anti-bonding in Pnm21-arsenic
are shown in Fig.?3. A three-dimensional representation of bonds and anti-bonds around As1 atom in Pnm21-As
is indicated in Extended Data Fig.?1. Anti-bonding is observed only among atoms in each layer. Van der Waals
bonding is observed in intralayer (As1?As4? and As4?As1?) and the remaining ones are in interlayer (e.g.
As1?As3, As2?As4? and As2?As3?).
Partial orbital-orbital correlations of the bond overlap populations in Pnm21-type arsenic crystal are
summarized in Extended Data Table?2. For covalent bonding (strong bonding), the contribution of pp hybridization is
the largest, and pd and sd have subsequent contributions. Bonding orbitals retain much of the p-like character.
Contribution of sp hybridization was not observed. For van der Waals bonding (weak bonding), contributions of
sd and pd hybridization are important, and pp has subsequent contributions. It is shown that d-orbitals contribute
greatly in covalent bonds and especially in van der Waals bonds. The d electrons are also responsible for cohesion.
Absolute values of partial orbital-orbital correlations for anti-bonding are usually larger than those for van der
Waals bonding. Bond overlaps are particularly small in the As1-As3 and As2-As4 van der Waals bonds.
The electron configuration of As is 4s2 3d10 4p3. Atomic net charge and contributions of each orbital to atomic
charge in Pnm21-As crystals are summarized in Table?1. The most important result is that total charges are clearly
divided into positive and negative in the As1, As1?, As2, As2? and As3, As3?, As4, As4? portions, respectively. The
deviation from 5.000 of the average charge of all atoms indicates electron transfer. Total charges of 4.97 for As2
and of 5.02 for As3 correspond to positive and negative charges of +0.03 and ?0.02, respectively. The clear
division of these net charges is caused by the difference in contribution of d orbitals. The contribution of d to the total
charge is clearly less in As1, As1?, As2, As2? portion corresponding to the R3 m-As structure part. The
contribution of s + p in As1, As1?, As2, As2? portion increases so as to compensate for the decrease in the contribution of
d. The contribution of the s orbital is largest in As1As1?, and the contribution of p orbital is largest in As2As2?.
Simulation results show unique electronic states in Pnm21-As.
experimental information around Fermi level by XANes. Figure?4a compares observed XANES
(X-ray absorption near edge structure) spectrum near the As K-edge for the Pnm21-type arsenic to that of R3
mtype arsenic. These spectra are similar, but clear differences are detected. The energy at half-maximum height
position (11.8611 keV) near the absorption edge for Pnm21-type arsenic shifts by 1.2 eV to the higher energy side
compared with 11.8599 keV for R3 m-type arsenic. This appears due to the electronic state change in the vicinity
of the Fermi level and the increase in the partial cationic bonding characteristic (donating electrons) in the
Pnm21-type arsenic. The observed chemical shift of 1.2eV in the XANES profile for Pnm21-type may correspond
to the simulation results (Table?1).
Details in XANES spectra can be examined more precisely by differential of XANES profile by photon energy
(dXANES). Figure?4b shows dXANES profiles for Pnm21-type and R3 m-type arsenic phases. The threshold
energy of absorption edge for each element is usually defined at the maximum peak position in the dXANES
profile. This is a position showing the maximum gradient at the absorption edge. Threshold energy (the
absorption edge) shifts to the higher energy side with increasing arsenic oxidation state. However, both threshold
energies found by the maximum values in dXANES spectrum (11.8623 keV) and the main peak position (11.8645 keV)
in XANES spectra (Fig.?4a) show identical values in these phases, indicating that the chemical bonding as the sum
of arsenic atoms in the Pnm21-type and R3 m-type phases is the same.
structure control (with layer stacking and twin) and band gap. The discovered third crystalline
form of arsenic (Pnm21-type As, parasenolamprite) is a novel structure in which basic parts of R3 m- and Bmab-As
are regularly arranged (Fig.?1b). Simulation results shows that the R3 m-part (As1As2 portion) is positively
charged by releasing electrons and the Bmab-As part (As3As4 portion) is charged negatively by receiving
electrons (Table?1). Net charges are clearly divided into positive and negative portions, Different characteristic parts
coexist in a single element crystal. Each part continues indefinitely in parallel to the b-axis. Both parts are
regularly arranged in the a-axial direction in the layer. Since the twin boundary runs parallel to the b-axis (Fig.?2),
introduction of twin enables control of various types of basic partial periodicity inter and intra layer without
changing the periodicity in the direction parallel to the b axis,.
The van der Waals bond distances between the adjacent layers are rich in variety from 3.12? in R3 m-As to
3.81 ? in Bmab-As. Contributions of sd and pd hybridization are most important for van der Waals bonding
(Table?1). The van der Waals bonding distance and the contribution of the d orbitals change along with change in
the stacking of layers in c-direction. This indicates that properties can be changed by control of layer stacking. The
features of this structure are interesting to both material science and crystallography. Grey semi-metallic arsenic
is an electric conductor, while black arsenic is a poor electric conductor. When grey semi-metal arsenic is
amorphized, it becomes a semiconductor with a band gap of 1.2 to 1.4 eV4. The arsenic system allows creation of
amorphous phases and some amorphous forms of arsenic exist. Discussions of amorphous-As have noted that physical
properties change due to expansion of the interlayer spacing and additional disordering within the layers13. This
corresponds well with our results, suggesting the importance of the contribution of d orbitals.
possibility for quantum materials: positively and negatively charged rods in two-dimensional
structure. Several kinds of ?organic superconductors? and ?synthetic metals? were made by combining
organic compounds or organic compounds with inorganic ions. Most were structures in which positively and
negatively charged layers were stacked separately. The charge transfer complex called TTF:TCNQ with a
column structure of tetrathiafulvalene (TTF) and tetracyanoquinodimethane (TCNQ) portions is known as a
synthetic highly conductive donor-acceptor complex17. Discovery of the Pnm21-As structure seems to be of some
importance. Total charges are clearly divided into positive and negative in the same elements for the grey-As and
black-As portions and the sequence in which one-dimensional electron donor and electron acceptor rods (parts)
alternate in the layer is the first description. The ability to design chemical bonding and atomic arrangement
within layers should open up further possibilities for the creation of new devices. Several phases of group-V
elements show superconductivity as quantum physical properties7?9. Group V elements offer various possibilities to
assemble new structures and control chemical bonding states and physical properties.
Unique physical characteristics can be expected not only as a three-dimensional structure but also as a
two-dimensional structure. Phospholene as a single layer of layered structure has been proposed as a promising
device10. Semi-metallic R3 m-phosphorous and black Bmab (Cmca)-phosphorus have structures similar to
grey-As and black-As, respectively. Phosphorus, an atom in the third period, also uses the d-orbital in some cases
depending on interactions with the electron shell of the binding partner. The 3d orbital in phosphorus, in addition
to 3 s and 3p orbitals, may also take part in the bonding of crystalline forms by constructing hybridized orbitals.
Regarding phosphorus and antimony, we would like to mention the possibility of controlling arrays in the layer
with two kinds of portions similar to the Pnm21-As phase. The possibility of two-dimensional materials in which
one-dimensional electron donors and electron acceptor rods alternate in a layer may be expected as a quantum
sample and chemical composition. Pararsenolamprite, the third natural crystalline polymorph of As,
was found in a dump of hydrothermal ore deposits of the Mukuno mine, Oita, Japan1. We found suitable
pararsenolamprite crystals for single crystal structure analysis in a specimen of parallel aggregates of bladed crystals from
a National Science Museum sample (sample No.NSM-28015). The crystals are lead-like dark grey in colour and
opaque with metallic lustre. The crystal samples have clear crystal faces and perfect cleavage. Pararsenolamprite
is sectile and brittle with perfect cleavage on . Euhedral crystals elongated on  and flattened on (001).
A pararsenolamprite single crystal of dimensions 27 ? 39 ? 17 ? m was cut and removed from euhedral crystal
aggregate for use with single-crystal structure analysis. Its chemical composition of As0.97Sb0.03 was determined
by JEOL scanning electron microscope SEM JSM-7001F and Oxford energy dispersive X-ray analyser EDS INCA
SYSTEM. This value is consistent with those reported by Matsubara et al.1. The arsenic crystal of this mine is
characterized by including small amounts of Sb.
Crystal structure analysis. Space group orthorhombic Pnm21 and lattice constants, a = 10.1193(
), c=10.3152 (
) ? were determined by RIGAKU XtaLAB SuperNova using graphite-monochromatized
MoK? radiations and a four-circle diffractometer using synchrotron radiation at beamline BL-10A of PF, KEK18,19.
Each crystallographic datum is shown in Extended data Table?1. A total of 3371 reflections were collected, and the
data were corrected for absorption effect and Lorentz and polarization factors. After initial structures were solved
by direct method, 742 unique reflections were used for refinement with |Fo| ? 4?(|Fo|) by full matrix-least-square
method. The structure was determined with the ShelXT solution program using Intrinsic Phasing and refined with
the ShelXL refinement package using least-squares minimisation20. After the least-square refinements, each R index
(=?||Fo| ?? |Fc||/?|Fo|) was convergence of 0.0575 using isotropic temperature factors. Positional parameters and
isotropic thermal displacement parameters are given in Extended data Table?2. The crystal structure was illustrated
XANes measurements. X-ray absorption near edge-structure (XANES) spectroscopy is effective for
electro structure characterisations. Spectra near the As K-edge for Pnm21-type and R3 m-type arsenic were collected
in fluorescence mode using a Lytle-type detector. Measurements were performed with a Si(111) double crystal
monochromater at BL-9C blanch lines of the Photon Factory at the High Energy Accelerator Research
Organization (KEK), Tsukuba, Japan. Mirrors were used to eliminate higher harmonics. X-ray energy calibration
was performed by setting the copper metal pre-edge absorption peak to 8978.8 eV. Details of the measurements
and analyses are given by Yoshiasa et al.22,23 and Sakai et al.24. Figure?4a,b compare the observed XANES spectrum
near the As K-edge and the differential of XANES profile by photon energy (dXANES) for Pnm21-type arsenic
with those for R3 m-type arsenic.
First principles calculations. Theoretical works have been performed to understand bonding
characteristics of Pnm21-type arsenic based on the first-principles computational method25. Electronic states were calculated
by the projector augmented-wave (PAW) method within the framework of density functional theory (DFT)26.
The generalized gradient approximation (GGA) functional proposed by Perdew, Burke and Ernzerhof27 was
employed for the exchange-correlation energy. The DFT-D method was employed for semiempirical correction
of the van der Waals interaction28. The momentum-space formalism was utilized, where the plane-wave cutoff
energies are 11.0 and 70.0 Ry for the electronic pseudo-wave function and the pseudo-charge density,
respectively29. The energy was minimized with respect to the Kohn-Sham orbitals iteratively using a preconditioned
conjugate-gradient method30. Projector functions were generated for the 4 s, 4p and 4d states as the valence states
for arsenic atoms. Periodic boundary conditions were applied to all Cartesian directions. Structural optimization
was performed using the experimentally determined crystallographic data of the orthorhombic unit cell
containing 16 atoms, which are listed in Extended Data Table?4. The optimized unit cell constants (?) were a= 10.1594,
b = 3.6649 and c = 10.3882. Monkhorst-Pack grids of 2 ? 6 ? 2 k points were used for Brillouin zone sampling. We
obtained the minimum-energy atomic configuration under 0.0 GPa using the quasi-Newton method. Calculated
lattice constants and atomic coordinates are in good agreement with our experimental results. The atomic net
charge of each atom and bond overlap populations between each atomic pair were calculated based on the
population analysis method31.
A. Yoshiasa and K. Sugiyama wrote the main manuscript text. A. Yoshiasa, M. Tokuda, K. Momma, A. Nakatsuka
and K. Sugiyama contributed to structure analyses and XANES experiments. M. Misawa and F. Shimojo were in
charge of the simulation. R. Miyawaki and S. Matsubara conducted chemical analyses, sample preparation and
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Additional Information Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-019-42561-8.