Kunio Miki

A simplest isolable monocyclic thiepin. Synthesis, structure, and thermal stability of 2,7-di-tert-butylthiepin

Abstract As an example of a simplest isolable monocyclic thiepin, 2,7-di-tert-butylthiepin (2) has been synthesized from 2,6-di-tert-butylthiopyrylium salt, and the thermal properties together with the X-ray crystal structure of (2) have been examined.

The preparation and X-ray molecular structure of a novel dialkylpalladium(II) compound containing bridged thiophenoxymethyl groups

Abstract A stable homoleptic palladium compound, [Pd(CH 2 SC 6 H 5 ) 2 ] 4 was isolated by treatment of (C 6 H 5 CN) 2 PdCl 2 with LiCH 2 SC 6 H 5 , and its molecular structure has been determined by means of three-dimensional X-ray diffraction data at −160°C. The CH 2 Cl 2 solvate ([Pd(CH 2 SC 6 H 5 ) 2 ] 4 · CH 2 Cl 2 ) forms orange-yellow, monoclinic crystals; a 16.302(3), b 19.394(4), c 18.552(3)A and β 91.28(2)° at −160°C, space group P 2 1 / n with Z = 4. The structure was solved by the conventional heavy atom method, and refined by the least-squares procedure to R = 0.089 for 4363 independent non-zero reflections. The fairly rigid cyclic tetramer is formed, which has approximate 222 symmetry. Four palladium atoms occupy the corners of a distorted rectangle and two averaged Pd···Pd distances are 4.051 and 3.304 A, respectively. Four coordination planes around the palladium atom, the geometries of which are essentially square-planar, are equivalent with each other. The CH 2 SC 6 H 5 groups bridge four palladium atoms (mean Sue5f8C(methylene) 1.82, Sue5f8C(phenyl) 1.80 A).

The molecular structure of chlorothiomethoxymethyltriphenylphosphinepalladium(II) at −160 and 20°C

Abstract The molecular structure of [PdCl(CH2SCH3)(PPh3)] has been determined from three-dimensional X-ray diffraction data collected at both −160 and 20°C. The crystal belongs to the monoclinic system, space group P21/c, with four formula units in a cell of dimensions: a 11.398(2), b 9.788(1), c 17.267(2) A and β 95.38(1)° at −160°C; a 11.454(3), b 9.880(2), c 17.459(2) A and β 95.84(1)° at 20°C. The structure was solved by the conventional heavy atom method, and refined by the least-squares procedure to R = 0.049 (−160°C) and 0.068 (20°C) for observed reflections. No essential difference is observed between molecular structures at −160 and 20°C. The geometry around the palladium atom is square-planar. The CH2SCH3 group, bonded to the palladium atom through Pdue5f8C and Pdue5f8S bonds, forms a metallocyclic three-membered ring [Pdue5f8C(1) 2.042(6), Pdue5f8S 2.371(1), Sue5f8C(1) 1.756(6) and Sue5f8C(2) 1.807(7) A, Pdue5f8C(1)ue5f8S 76.9(2), Pdue5f8C(1)ue5f8H 113(3) and 122(4)°, Sue5f8C(1)ue5f8H 115(3) and 112(4) and Hue5f8C(1)ue5f8H 113(5)° at −160°C].

The molecular structure of chlorothiomethoxymethyl-bis(triphenylphosphine)palladium(II) methylenechloride solvate at −160°C

Abstract The precise molecular structure of [PdCl(CH 2 SCH 3 )(PPh 3 ) 2 ] has been determined from three-dimensional X-ray diffraction data collected at −160°C. The CH 2 Cl 2 solvated crystal ([PdCl(CH 2 SCH 3 )(PPh 3 ) 2 · CH 2 Cl 2 ]) belongs to the monoclinic system, space group P 2 1 / n , with four formula units in a cell of dimensions: a 14.973(3), b 15.333(3), c 17.377(3) A and β 115.77(1)° at −160°C. The structure was solved by the conventional heavy atom method and refined by the least-squares procedure to R = 0.035 for observed reflections. The geometry around the palladium atom is square-planar. The phosphorus atoms of the two triphenylphosphine ligands are mutually trans . The CH 2 SCH 3 group is bonded to the palladium atom only through the Pdue5f8C σ-bond and the sulfur atom is not bonded to the metal atom (Pdue5f8C(1) 2.061(3), Sue5f8C(1) 1.796(3), Sue5f8C(2) 1.817(5), Pd⋯S 2.973(1) A, Pdue5f8C(1)ue5f8S 100.64(14)° and C(1)ue5f8Sue5f8C(2) 101.28(18)°). The structure is in contrast to that of [PdCl(CH 2 SCH 3 )(PPh 3 )], in which both the carbon and sulfur atoms of the CH 2 SCH 3 group are bonded to the palladium atom.

Crystallization and preliminary X-ray diffraction study of ferrocytochrome c2 from Rhodopseudomonas viridis

Crystals of ferrocytochrome c2 from a non-sulphur purple photosynthetic bacterium, Rhodopseudomonas viridis, have been grown from ammonium sulphate solution at pH 8.5 by the sitting-drop vapour-diffusion procedure. The crystals belong to the trigonal system, space group P3(1)21 (or its enantiomorph P3(2)21) with unit-cell dimensions of a = b = 75.8 A and c = 40.1 A, and diffract to at least 2.0 A resolution. Assuming that an asymmetric unit contains one protein molecule (approx. 12,300 Mr), the solvent content of the crystal is approximately 54.5% (v/v).

The molecular structure of a three-coordinate palladium(II)-styrene complex [Pd(η5-C5H5)(PEt3)(styrene)]BF4

Abstract The molecular structure of a three-coordinate palladium(II)-styrene complex, [Pd(η 5 -C 5 H 5 )(PEt 3 )(styrene)]BF 4 has been determined by means of X-ray diffraction. The crystal belongs to the monoclinic system, space group P 2 1 / c , with four formula units in a cell of dimensions: a 10.229(3), b 11.262(3), c 18.760(5) A and β 103.77(2)°. The structure was solved by the heavy atom method, and refined by the least-squares procedure to R = 0.050 for 3635 observed reflections. The palladium atom is surrounded by the cyclopentadienyl group, the triethylphosphine ligand and the olefinic bond of styrene in the cationic complex. In the palladiumue5f8styrene bonding, the olefinic bond is inclined by 77.3° to the coordination plane defined by the Pd and P atoms and the center of the cyclopentadienyl ring (Pdue5f8C(1) 2.176(6), Pdue5f8C(2) 2.234(5) and C(1)ue5f8C(2) 1.369(8) A).

Crystal structure of a methyl(methoxy)carbene complex of nickel(II), trans-[Ni(C6Cl5)(PMe2Ph)2{C(OMe)Me}]BF4

Abstract The structure of a nickel(II) complex, trans -[Ni(C 6 Cl 5 )(PMe 2 Ph) 2 {C(OMe)Me}]BF 4 , containing the simplest alkyl(alkoxy)carbene ligand has been determined by X-ray crystallography ( R = 0.091). The geometry around the nickel atom is square-planar. The comparatively short Niue5f8C(1) bond length of 1.843(10) A showed the presence of π-bonding in the nickel-carbene bond.

Preliminary crystallographic study of a ribulose-1,5-bisphosphate carboxylase-oxygenase from Chromatium vinosum

Crystals of a ribulose-1,5-bisphosphate carboxylase-oxygenase from Chromatium vinosum were obtained with the hanging-drop vapor diffusion technique, using polyethylene glycol 4000 as precipitant. The crystal belongs to the cubic system, space group I432, with unit cell dimension a = 245.9 A. An asymmetric unit includes one-quarter (L2S2, L: large subunit, S: small subunit) of a hexadecameric molecule (L8S8, 544,000 Mr), which is located on the crystallographic point symmetry 222 or 4. The crystal diffracts to at least 3.0 A resolution.

Crystal structures of a methylmethoxycarbene complex and the corresponding vinyl complex of nickel(II)

Abstract The molecular structures of nickel complexes containing the simples alkyl(alkoxy)carbene ligand or the corresponding vinyl ligand, rans -[Ni(C 6 Cl 5 )(PMe) 3 ) 2 -{C(OMe)Me}]BF 4 or trans -[Ni(C 6 Cl 5 )(PMe 3 ) 2 {C(OMe)ue5fbCH 2 }], respectively, have been determined by single-crystal X-ray diffraction. Crystals of the carbene complex are monoclinic, space group P 2 2 / n with Z = 4 in a unit cell of dimension a 13.382(7), b 11.173(5), c 16.599(6) A, β 107.95(4)° at −100°C. Crystals of the vinyl complex are also monoclinic, space group P 2 1 / n with Z = 4 in a unit cell of dimensions a 9.255(2), b 9.265(2), c 26.779(4) A, β95.06(2)° at 20°C. Structures were refined to R = 0.072 (4318 reflections) and R = 0.052 (3766 reflections) for the carbene and the vinyl complexes, respectively. The coordination geometry around the Ni atom is typically square-planar in each complex. The methylmethoxy carbene ligand is disordered even at −100°C in the crystal of the carbene complex. The Niue5f8C(carbene) bond (1.848 A) is about 0.07 A shorter than the coresponding Niue5f8C(vinyl) bond (1.916 A). On the other hand, Niue5f8P bond lengths in the carbene complex (2.212 A) are about 0.03 A longer than those in the vinyl complex (2.178 A). These facts indicate significantly the presence of π back-bonding in the Niue5f8C(carbene) bond in trans -[Ni(C 6 Cl 5 )(PMe 3 ) 2 {C(OMe)Me}BF 4 .

The molecular structure of a thia-allyl palladium complex at—160°C and 20°C

Abstract The molecular structure of a novel palladium complex containing a thia-allyl group has been determined from three-dimensional X-ray diffraction data collected at both −160°C and 20°C. The crystal belongs to the monoclinic system, space group P21/n, with four formula units in a cell of dimensions: a 8.752(3), b 11.444(4), c 19.095(5) A and β 92.06(3)° at −160°C; a 8.801(1), b 11.562(2), c 19.390(2) A and β 91.53(1)° at 20°C. The structure was solved by the heavy atom method, and refined by the least-squares procedure to R ue5fb 0.033 (−160°C) and 0.039 (20°C) for non-zero reflections. No essential difference is observed between molecular structures at −160 and 20°C. The coordination mode of the thia-allyl group ((MeOCO)2CHCH2(Me)C(Me2N)Cue5fbS), which is bound to the palladium atom through the Pdue5f8C σ-bond and the donation of the sulfur atom to the metal atom, is not a π-type but a σ-type [Pdue5f8C(7) 2.058(3), Pdue5f8S 2.262(1), C(6)–C(7) 1.506(4) and C(6)ue5f8S 1.709(3) A at −160°C]. The relatively short Pdue5f8S bond may show strong donation of the sulfur to the metal atom. The geometry around the palladium atom is essentially square-planar. The C(6), C(7) and S atoms in the thia-allyl group are almost coplanar with the palladium atom.