Se Bond Lengths Research Articles

Peculiar bond length dependence in (Ag,Cu)GaSe2 alloys and its impact on the bandgap bowing

Contrary to other semiconductor alloys, incorporation of Ag into CuGaSe2 increases the bandgap, even though the lattice expands, and the Ga–Se bond length is theoretically predicted to decrease rather than increase. Herein, we experimentally confirm this peculiar bond length dependence of (Ag,Cu)GaSe2 using x-ray absorption spectroscopy. We further model the different anion displacements and estimate that their combined contribution to the bandgap bowing is close to zero. These findings differ from those for Cu(In,Ga)Se2 and demonstrate the diversity of chalcopyrite alloys and their properties.

Structural, electronic and magnetic properties of TlFeSe2 under high pressure

The high-pressure (HP) properties of TlFeSe2 are investigated based on the first-principles calculations combined with structure-searching method. The low-pressure C2/m phase will transform into the orthorhombic Pnma phase at 2 GPa, with 8% volume collapse, the insulator–metal transition and the bicollinear antiferromagnetic-to-nonmagnetic spin-crossover. At pressure higher than 8 GPa, the HP C2/m phase will become the ground state. Both Pnma phase and HP C2/m phase are constituted by one-dimensional chains of edge-sharing FeSe5 tetragonal pyramids. Pressuring decrease the Se–Se bond length giving rise to the transition from [Se2]3− to [Se2]2−. Negative charge transfer causes the Fe2+ with ∼2 μ B magnetic moment at ambient pressure and the nonmagnetic Fe1.5+ at higher pressure. The Fermi surfaces of HP phases are also discussed.

Effect of band structure adjustment based of Cu site on the thermoelectric properties of BiCuSeO

The effect of Ti doped at Cu site on the thermoelectric properties of BiCuSeO was studied by experimental method and first principles calculation. The samples were prepared by high-temperature solid-state reaction, mechanical alloying and spark plasma sintering. The results show that Ti doping can cause the lattice contraction and decrease the lattice constant. Ti doping can increase the bandgap and lengthen the Cu/Ti–Se bond, resulting in the decrease of carrier concentration. Ti doping can reduce the effective mass and the Bi–Se bond length, correspondingly improve the carrier mobility. Ti doping can decrease the density of states of Cu-3d and Se-4p orbitals at the top of valence band, but Ti-4p orbitals can obviously increase the density of states at the top of valence band and finally increase the electrical conductivity in the whole temperature range with the highest value of 192 Scm−1 at 873 K. With the decrease of effective mass, Ti doping would reduce the Seebeck coefficient, but the gain effect caused by the increase of electrical conductivity is more than the benefit reduction effect caused by the decrease of Seebeck coefficient, and the power factor shows an upward trend. Ti doping can reduce Young's modulus, lead to the increase of defect scattering and strain field for the heat-carrying phonons, correspondingly reduce the lattice thermal conductivity and total thermal conductivity. It is greatly increased for the ZT values in the middle- and high-temperature range, with the highest value of 1.04 at 873 K obtained by 4% Ti-doped sample.

Isolation and structure of an 18-membered macrocycle containing two diselenide linkages and its precursor.

The structures of the 18-membered diselenide-linked macrocycle 10,27-di-tert-butyl 11,28-dioxo-2,3,19,20-tetraselena-10,12,27,29-tetraazapentacyclo[28.4.0.04,9.013,18.021,26]tetratriaconta-1(30),4(9),5,7,13,15,17,21,23,25,31,33-dodecaene-10,27-dicarboxylate, C36H34N4O6Se4, and its precursor di-tert-butyl 2,2'-[diselane-1,2-diylbis(2,1-phenylene)]dicarbamate, C22H28N2O4Se2, are reported. The precusor to the macrocycle contains two tert-butyl phenylcarbamate arms connected to a diselenide group, with Se-C and Se-Se bond lengths of 1.914 (4) and 2.3408 (6) Å, respectively. The macrocycle resides on a crystallographic center of inversion in space group P-1 with one molecule in the unit cell (Z' = 1/2). It contains an 18-membered macrocyclic ring with two diselenide linkages. In this macrocycle, there are two free and two protected amino groups.

Coordination of 1-methyl-1,3-dihydro-2H-benzimidazole-2-selone to zinc and cadmium: Monotonic and non-monotonic bond length variations for [H(sebenzimMe)]2MCl2 complexes (M = Zn, Cd, Hg)

The reactions of 1-methyl-1,3-dihydro-2H-benzimidazole-2-selone, H(sebenzimMe), towards the zinc and cadmium halides, MX2 (M = Zn, Cd; X = Cl, Br, I), afford the adducts, [H(sebenzimMe)]2MX2, which have been structurally characterized by X-ray diffraction. The halide ligands of each of these complexes participate in hydrogen bonding interactions with the imidazole N–H moieties, although the nature of the interactions depends on the halide. Specifically, the chloride and bromide derivatives, [H(sebenzimMe)]2ZnX2 and [H(sebenzimMe)]2CdX2 (X = Cl, Br), exhibit two intramolecular N–H⋯X interactions, whereas the iodide derivatives, [H(sebenzimMe)]2ZnI2 and [H(sebenzimMe)]2CdI2, exhibit only one intramolecular N–H⋯I interaction. Comparison of the M–Se and M–Cl bond lengths of the chloride series, [H(sebenzimMe)]2MCl2 (M = Zn, Cd, Hg), indicates that while the average M–Cl bond lengths progressively increase as the metal becomes heavier, the variation in M–Se bond length exhibits a non-monotonic trend, with the Cd–Se bond being the longest. These different trends provide an interesting subtlety concerned with use of covalent radii in predicting bond length differences. In addition to tetrahedral [H(sebenzimMe)]2CdCl2, [H(sebenzimMe)]3CdCl2·[H(sebenzimMe)]4CdCl2, which features both five-coordinate and six-coordinate coordinate centers, has also been structurally characterized. Finally, the reaction between CdI2 and H(sebenzimMe) at elevated temperatures affords the 1-methylbenzimidazole complex, [H(sebenzimMe)][H(benzimMe)]CdI2, a transformation that is associated with cleavage of the C–Se bond.

Hypervalent organoselenium compounds stabilized by intramolecular coordination: synthesis and crystal structures.

Two novel hypervalent selenium(IV) compounds stabilized by intramolecular interactions, namely 6-phenyl-6,7-dihydro-5H-2,3-dioxa-2aλ4-selenacyclopenta[hi]indene, C14H12O2Se, 14, and 5-phenyl-5,6-dihydro-4H-benzo[c][1,2]oxaselenole-7-carbaldehyde, C14H12OSe2, 15, have been synthesized by the reaction of 2-chloro-1-formyl-3-(hydroxymethylene)cyclohexene with in-situ-generated disodium diselenide (Na2Se2). The title compounds were characterized by FT-IR spectroscopy, ESI-MS, and single-crystal X-ray diffraction studies. For 14, there is whole-molecule disorder, with occupancies of 0.605 (10) and 0.395 (10), a double bond between C and Se, and the five-membered selenopentalene rings are coplanar. The packing is stabilized by π-π stacking interactions involving one of the five-membered Se/C/C/C/O rings [centroid-centroid (Cg...Cg) distance = 3.6472 (18) Å and slippage = 1.361 Å], as well as C-H...π interactions involving a C-H group and the phenyl ring. In addition, there are bifurcated C-H...Se,O interactions which link the molecules into ribbons in the c direction. For 15, the C-Se bond lengths are longer than those of 14. The two five-membered rings are coplanar. There are no π-π or C-H...π interactions; however, molecules are linked by C-H...O interactions into centrosymmetric dimers, with graph-set notation R22(16).

An Assessment of Computational Methods for Calculating Accurate Structures and Energies of Bio-Relevant Polysulfur/Selenium-Containing Compounds.

The heavier chalcogens sulfur and selenium are important in organic and inorganic chemistry, and the role of such chalcogens in biological systems has recently gained more attention. Sulfur and, to a lesser extent selenium, are involved in diverse reactions from redox signaling to antioxidant activity and are considered essential nutrients. We investigated the ability of the DFT functionals (B3LYP, B3PW91, ωB97XD, M06-2X, and M08-HX) relative to electron correlation methods MP2 and QCISD to produce reliable and accurate structures as well as thermochemical data for sulfur/selenium-containing systems. Bond lengths, proton affinities (PA), gas phase basicities (GPB), chalcogen–chalcogen bond dissociation enthalpies (BDE), and the hydrogen affinities (HA) of thiyl/selenyl radicals were evaluated for a range of small polysulfur/selenium compounds and cysteine per/polysulfide. The S–S bond length was found to be the most sensitive to basis set choice, while the geometry of selenium-containing compounds was less sensitive to basis set. In mixed chalcogens species of sulfur and selenium, the location of the sulfur atom affects the S–Se bond length as it can hold more negative charge. PA, GPB, BDE, and HA of selenium systems were all lower, indicating more acidity and more stability of radicals. Extending the sulfur chain in cysteine results in a decrease of BDE and HA, but these plateau at a certain point (199 kJ mol−1 and 295 kJ mol−1), and PA and GPB are also decreased relative to the thiol, indicating that the polysulfur species exist as thiolates in a biological system. In general, it was found that ωB97XD/6-311G(2d,p) gave the most reasonable structures and thermochemistry relative to benchmark calculations. However, nuances in performance are observed and discussed.

Co2+-Doping of Magic-Sized CdSe Clusters: Structural Insights via Ligand Field Transitions

Magic-sized clusters represent materials with unique properties at the border between molecules and solids and provide important insights into the nanocrystal formation process. However, synthesis, doping, and especially structural characterization become more and more challenging with decreasing cluster size. Herein, we report the successful introduction of Co2+ ions into extremely small-sized CdSe clusters with the intention of using internal ligand field transitions to obtain structural insights. Despite the huge mismatch between the radii of Cd2+ and Co2+ ions (>21%), CdSe clusters can be effectively synthesized with a high Co2+ doping concentration of ∼10%. Optical spectroscopy and mass spectrometry suggest that one or two Co2+ ions are substitutionally embedded into (CdSe)13 clusters, which is known as one of the smallest CdSe clusters. Using magnetic circular dichroism spectroscopy on the intrinsic ligand field transitions between the different 3d orbitals of the transition metal dopants, we demonstrate that the Co2+ dopants are embedded on pseudotetrahedral selenium coordinated sites despite the limited number of atoms in the clusters. A significant shortening of Co-Se bond lengths compared to bulk or nanocrystals is observed, which results in the metastability of Co2+ doping. Our results not only extend the doping chemistry of magic-sized semiconductor nanoclusters, but also suggest an effective method to characterize the local structure of these extremely small-sized clusters.

Phase Modulation of (1T-2H)-MoSe2/TiC-C Shell/Core Arrays via Nitrogen Doping for Highly Efficient Hydrogen Evolution Reaction.

Tailoring molybdenum selenide electrocatalysts with tunable phase and morphology is of great importance for advancement of hydrogen evolution reaction (HER). In this work, phase- and morphology-modulated N-doped MoSe2 /TiC-C shell/core arrays through a facile hydrothermal and postannealing treatment strategy are reported. Highly conductive TiC-C nanorod arrays serve as the backbone for MoSe2 nanosheets to form high-quality MoSe2 /TiC-C shell/core arrays. Impressively, continuous phase modulation of MoSe2 is realized on the MoSe2 /TiC-C arrays. Except for the pure 1T-MoSe2 and 2H-MoSe2 , mixed (1T-2H)-MoSe2 nanosheets are achieved in the N-MoSe2 by N doping and demonstrated by spherical aberration electron microscope. Plausible mechanism of phase transformation and different doping sites of N atom are proposed via theoretical calculation. The much smaller energy barrier, longer HSe bond length, and diminished bandgap endow N-MoSe2 /TiC-C arrays with substantially superior HER performance compared to 1T and 2H phase counterparts. Impressively, the designed N-MoSe2 /TiC-C arrays exhibit a low overpotential of 137 mV at a large current density of 100 mA cm-2 , and a small Tafel slope of 32 mV dec-1 . Our results pave the way to unravel the enhancement mechanism of HER on 2D transition metal dichalcogenides by N doping.

3,3′-[(2-Bromo-1,3-phenylene)bis(methylene)]bis(1-butyl-2,3-dihydro-1H-imidazole-2-selone)

In the title compound, C22H29BrN4Se2, the two Se atoms are directed in opposite directions with respect to the central benzene ring. The C=Se bond lengths at 1.848 (5) and 1.851 (5) Å are on the long side for a double bond but shorter than expected for a C—Se single bond. In the crystal, Br...Br intermolecular interactions [3.4685 (12) Å] link the molecules into a zigzag chain propagating along theb-axis direction. In addition, there are C—H...Se intermolecular interactions present, linking the chains to form slabs parallel to theabplane. One of the two butyl side chains is disordered over two conformations with occupancies of 0.777 (9) and 0.223 (9).

Indium selenide monolayer: strain-enhanced optoelectronic response and dielectric environment-tunable 2D exciton features

Electronic and optical performances of the β-InSe monolayer (ML) are considerably boosted by tuning the corresponding band energies through lattice in-plane compressive strain engineering. First principles calculations show an indirect–direct gap transition with a large bandgap size. The crossover is due to different responses of the near-gap state energies with respect to strain. This is explained by the variation of In–Se bond length, the bond nature of near-band-edge electronic orbital and of the momentum angular contribution versus in-plane compressive strain. The effective masses of charge carriers are also found to be highly modulated and significantly light at the indirect–direct-gap transition. The tuned optical response of the resulting direct-gap ML β-InSe is evaluated versus applied energy to infer the allowed optical transitions, dielectric constants, semiconductor–metal behavior and refractive index. The environmental dielectric engineering of exciton behavior of the resulting direct-gap ML β-InSe is handled within the effective mass Wannier–Mott model and is expected to be important. Our results highlight the increase of binding energy and red-shifted exciton energy with decreasing screening substrates, resulting in a stable exciton at room temperature. The intensity and energy of the ground-state exciton emission are expected to be strongly influenced under substrate screening effect. According to our findings, the direct-gap ML β-InSe assures tremendous 2D optoelectronic and nanoelectronic merits that could overcome several limitations of unstrained ML β-InSe.

Effect of P-Containing Ligands on the Structural and Optical Properties of (CdSe)n (n = 3, 6, 10) Clusters

The effect of phosphorus-containing ligands on the structure, energetics and properties of the (CdSe)n clusters (n = 3, 6, and 10) with different number of PH3 and PMe3 ligands were studied by using density functional theory calculations. The P atom in the ligand interacts with Cd and forms a strong Cd–P coordination bond. The introduction of ligands does not change the cluster architecture, but leads to considerable changes in Cd–Se bondlength, charge distribution, binding energy, HOMO–LUMO gap and optical absorption. The ligand influence is enhanced with increasing ligand coverage. A blueshift in absorption band was predicted for the clusters with increasing ligands, resulting from the electron donating characteristics of the ligands that hamper electron transition from Se to Cd. As P-containing ligands are often used in the preparation of CdSe nanocrystals, our calculations reveal the influence of ligand-cluster interaction on the cluster geometrical and electronic properties, which would be helpful for the nanocrystal design and synthesis.

Tris(4-methoxyphenyl)phosphine selenide

The title compound, C21H21O3PSe, is comprised of a P atom in a distorted tetrahedral environment, attached to the Se atom and three C atoms of the phenyl rings. The P—Se bond length is 2.1214 (12) Å. All three methoxy groups are near coplanar with their respective phenyl rings, with the angles between the phenyl ring and the C—O bond of the methoxy groups being 5.7 (2), 1.5 (4), and 5.7 (3)°. The torsion angles of the phenyl rings relative to the P=Se bond are 35.62 (10), 35.07 (13), and 44.50 (11)°. No strong intermolecular interactions were observed, but that in addition to van der Waals forces, there are C—H...π and C—H...Se close contacts.

Polymeric Complex of 1‐Phenylsulfanyl/selenylmethyl‐1H‐Benzotriazole with Ag(I): Pre–catalystfor A3 Coupling Affording Propargylamines on aGram/Lab Scale

AbstractA3 coupling of aldehyde, amine and phenylacetylene catalyzed with [AgL1/L2(amine)]+ generated in situ from a polymeric complex[{Ag(μ‐L1/L2)NO3}n] where L1=1‐phenylsulfanylmethyl‐1H‐benzotriazole and L2=1‐phenylselenylmethyl‐1H‐benzotriazole) was found suitable for gram and lab scale synthesis of propargylamines (Yield up to 88 and 94 %, respectively) at 60 °C in 3 h. The catalytic process is simple and applicable to various combinations of aldehyde and amine substrates. 1‐Chloromethyl‐1H‐benzotriazole was reacted with PhSNa and PhSeNa, generated in situ, to prepare ligands L1 and L2, respectively. The reactions of AgNO3 with L1 and L2in acetonitrile at 70 °C resulted in [{Ag(μ‐L)NO3}n] (1 and 2,when L=L1 and L2respectively), stable under ambient conditions including light. The ligands and complexes have been characterized with 1H, 13C{1H} and 77Se{1H} NMR spectroscopy and mass spectrometry. The single crystal structures of 1 and 2 have been determined by X‐ray diffraction. The Ag–S and Ag–Se bond lengths in 1 and 2are 2.466(2) and 2.5334(17) Å, respectively.

Study of Electronic and Optical Properties of CuInSe2 Nanowires

The electronic and optical properties of the CuInSe2 nanowires have been investigated via density functional theory. We have used numerical atomic orbital bases set with local-density approximation. The norm-conserving pseudopotentials of Troullier and Martins have been used. In our calculation we used nanowires in two shapes of hexagonal and triangular with their diameters ranging from 8 to 15 A in the (1–10) growth direction. The geometrical parameters are in good agreement compared with other experimental or theoretical results. We show that for the nanowires there is a significant contraction of the Cu–Se and In–Se bond lengths at the edge of the wires (4.7%); as for the wires at the center, it is 2.6%. Moreover, we have investigated the band structures and atom-projected density of states of the nanowires. These studies confirm that CuInSe2 nanowires are semiconductors with a direct band gap. These studies also show the existence of hybridization between Cu-d with Se-p states in the middle valence su...

Pyrazole‐Stabilized Dinuclear Palladium(II) Chalcogenolates Formed by Oxidative Addition of Bis[2‐(4‐bromopyrazol‐1‐yl)ethyl] Dichalcogenides to Palladium(II) – Tailoring of Pd–S/Se Nanoparticles

AbstractBis[2‐(4‐bromopyrazol‐1‐yl)ethyl] disulfide and diselenide L1 and L2 were synthesized by the reactions of 4‐bromo‐1‐(2‐chloroethyl)‐1H‐pyrazole with the in situ generated Na2S2 and Na2Se2. The reactions of L1 and L2 with 2 equiv. of [PdCl2(CH3CN)2] in CH3CN at 70 °C proceed through an oxidative addition/reductive elimination sequence to the PdII center to form the chalcogenolato‐bridged dinuclear palladium(II) complexes [Pd2Cl2(μ‐EN)2] [1 (E = S) and 2 (E = Se); EN = 2‐(4‐bromopyrazol‐1‐yl)ethanechalcogenolate]. The reactions of 1 and 2 with CH3CN and AgBF4 resulted in the formation of [Pd2(CH3CN)2(μ‐EN)2]·2BF4 (3 and 4). Compounds L1, L2, and their complexes 1–4 have been characterized through 1H, 13C{1H}, and 77Se{1H} nuclear magnetic resonance (NMR) spectroscopy; infrared (IR) spectroscopy; and high‐resolution mass spectrometry (HRMS). The single‐crystal X‐ray structures of 2–4 have revealed distorted square‐planar geometries around the Pd center in each case. The Pd–S and Pd–Se bond lengths are in the ranges 2.277(2)–2.296(2) and 2.372(9)–2.3971(17) Å, respectively. Single‐source precursor routes for the synthesis of palladium chalcogenide nanoparticles (NPs) have been developed by the thermolyses of 1–4 in 1:1 mixtures of oleic acid (OA) and 1‐octadecene (ODE). Pd17Se15 NPs were formed from both PdII selenolates 2 and 4, whereas Pd4S NPs and a mixture of Pd16S7 (ca. 68 %) and PdS (ca. 32 %) NPs were obtained from PdII thiolates 1 and 3, respectively. Transmission electron microscopy (TEM), scanning electron microscopy with energy‐dispersive X‐ray spectroscopy (SEM‐EDX), and powder X‐ray diffraction (PXRD) have been used to authenticate the NPs. X‐ray photoelectron spectroscopy (XPS) studies on the NPs have revealed that there is a charge transfer from Pd to S/Se. The compositions of the NPs determined from XPS are consistent with the PXRD results.

Long-lived emission in Mn doped CdS, ZnS, and ZnSe diluted magnetic semiconductor quantum dots

Slow luminescence is studied in Mn doped CdS, ZnS, and ZnSe quantum dots. Because of the high degeneracy of Mn d-orbitals, we employ the multi-determinant SAC–CI computational method to determine the spin-forbidden transition from the 4T1 first excited to 6A1 ground state. We find that the transition energies for each material are in the excellent agreement with the experimental data. The computations reveal that the absorption spectra are independent of the presence of Mn impurities in quantum dots. The calculations show that the Mn impurity levels are located inside the QD gaps and the slow emission energies are independent of QD sizes. These features allow us to conclude that there are two luminescence peaks in the spectrum with fast (the higher energy) and slow (the lower energy) relaxations. In experiments sometimes the fast luminescence band disappears. This effect depends on Mn concentrations and a doping method. For different QD crystal structures the Mn–S (Se) bond lengths can vary. Therefore we find that the slow luminescence energy is very sensitive to a bond length. Indeed if we change the Mn–S bond length by 0.1Å, the energy increases by 0.2eV within the calculated range of bond lengths.

Effect of van der Waals interactions on the structural and binding properties of GaSe

The influence of van der Waals interactions on the lattice parameters, band structure, elastic moduli and binding energy of layered GaSe compound has been studied using projector-augmented wave method within density functional theory. We employed the conventional local/semilocal exchange-correlation functionals and recently developed van der Waals functionals which are able to describe dispersion forces. It is found that application of van der Waals density functionals allows to substantially increase the accuracy of calculations of the lattice constants a and c and interlayer distance in GaSe at ambient conditions and under hydrostatic pressure. The pressure dependences of the a-parameter, Ga–Ga, Ga–Se bond lengths and Ga–Ga–Se bond angle are characterized by a relatively low curvature, while c(p) has a distinct downward bowing due to nonlinear shrinking of the interlayer spacing. From the calculated binding energy curves we deduce the interlayer binding energy of GaSe, which is found to be in the range 0.172–0.197eV/layer (14.2–16.2meV/Å2).

Palladium(ii) complexes bearing the 1,2,3-triazole based organosulfur/ selenium ligand: synthesis, structure and applications in Heck and Suzuki–Miyaura coupling as a catalyst via palladium nanoparticles

Air and moisture insensitive palladium complexes, [Pd(L)Cl2] (1/2), in which L = 1-benzyl-4-phenylthiomethyl or 1-benzyl-4-phenylselenomethyl-1H-1,2,3-triazole (L1 or L2) catalyze Heck (HC) and Suzuki–Miyaura coupling (SMC) reactions between a series of aryl bromides including deactivated bromides and n-butyl acrylate and phenylboronic acid, respectively. The optimal catalytic loading was found to be in the order of 0.01 mol%. HRTEM, TGA and EDX data indicated that 3–11 nm nanoparticles (NPs) composed of palladium and sulfur or selenium and protected with L or its fragment, were formed during the catalyzed reaction. The isolated NPs displayed catalytic activity and appeared to have a role in the catalysis. A two-phase test indicated that both homogeneous and heterogeneous catalysis took place. The complexes 1 and 2 were synthesized by the reactions of L1 and L2 respectively with [(MeCN)2PdCl2]. Their single crystal X-ray diffraction indicated that the geometry adopted by ligands around Pd in both complexes is distorted square planar with Pd–S and Pd–Se bond lengths of 2.2727(14) and 2.3693(8) Å, respectively. DFT calculation gave bond lengths and angles in keeping with the experimental values. The DFT calculated HOMO–LUMO energy difference is lower for 1 than for 2 in accordance with the observed higher catalytic activity of 1.

Local structures around3dmetal dopants in topological insulatorBi2Se3studied by EXAFS measurements

Transition-metal-doped ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ crystals, ${X}_{0.05}{\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ ($X=\mathrm{Cr}$, Co, Ni, and Cu), are prepared and studied by powder x-ray diffraction and extended x-ray absorption fine structure (EXAFS) measurements to get the local structures around the dopants. Cr atoms substitute Bi atoms and Co atoms may substitute Bi atoms or form ${\mathrm{Co}}_{3}{\mathrm{Se}}_{4}$ ($C2/m$) clusters. Cu is also found taking the Bi substitutional site, which differs from the reported superconductor phase of Cu-doped ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$, suggesting the dependence of site occupancy of Cu in ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ on the process of sample growing. For ${\mathrm{Ni}}_{0.05}{\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$, Ni atoms form ${\mathrm{Ni}}_{3}{\mathrm{Se}}_{4}$ ($C2/m$) clusters. The nearest neighbors of $X$ ($X=\mathrm{Cr}$, Co, and Cu) are Se atoms, and the $X$-Se bond lengths are extracted from EXAFS as 2.50 \AA{} for Cr-Se, 2.40 \AA{} for Co-Se, and 2.38 \AA{} for Cu-Se, which show the direct evidences of dramatic structural relaxations around $3d$ dopants. The bond information of local structures around dopants is valuable for subsequent theoretical studies, and can hardly be obtained from other techniques.