Heteropolytopic arsanylarylthiolato ligands: cis-trans isomerism of nickel(II), palladium(II), and platinum(II) complexes of 1-AsPh2-2-SHC6H4.

Heteropolytopic arsanylthiolato ligands 1-AsPh(2)-2-SHC(6)H(4) (AsSH), PhAs(2-SHC(6)H(4))(2) (AsS(2)H(2)), and As(2-SHC(6)H(4))(3) (AsS(3)H(3)) have been prepared by lithiation-electrophilic substitution procedures. The 2:1 reaction of AsSH with NiCl(2)·6H(2)O, Na(2)[PdCl(4)], and [PtI(2)(cod)] (cod = 1,5-cyclooctadiene) in the presence of NEt(3) afforded the square-planar complexes trans-[Ni{(AsS)-κ(2)S,As}(2)] (1), cis-[Pd{(AsS)-κ(2)S,As}(2)] (2), trans-[Pd{(AsS)-κ(2)S,As}(2)] (3), and cis-[Pt{(AsS)-κ(2)S,As}(2)] (4). In the cases of nickel and platinum, only one isomer was isolated. With palladium, initially the cis isomer 2 is formed and undergoes slow isomerization to the trans isomer 3 in solution. Small amounts of the trinuclear complex [{PtI(1-AsPh(2)-µ-2-S-C(6)H(4)-κ(2)S,As)}(3)] (5) are also formed besides the mononuclear platinum bis-chelate complex 4. Density functional theory calculations support a dissociative mechanism for the isomerization of the palladium(II) complexes.

Heteropolytopic phosphanylarylthiolato ligands: formation of cis isomers of nickel(II), palladium(III) and platinum(III) complexes with 1-P(Biph)-2-SHC6H4 (Biph = 1,1'-biphenyl-2,2'-diyl).

Reaction of the ditopic phosphanylarylthiol 1-P(Biph)-2-SHC(6)H(4) (BiphPSH, Biph = 1,1'-biphenyl-2,2'-diyl), prepared by lithiation-electrophilic substitution, with NiCl(2)·6H(2)O, Na(2)[PdCl(4)] and [PtI(2)(cod)] (cod = 1,5-cyclooctadiene) in a 2:1 ratio and in the presence of NEt(3) led to formation of exclusively cis isomers of the square-planar complexes cis-[M{(1-P(Biph)-2-S-C(6)H(4))-κ(2)S,P}(2)] ([M{(BiphPS)-κ(2)S,P}(2)]; M = Ni (1), Pd (2), Pt (3)). Density functional calculations support the assumption that this is probably due to intramolecular π-π interaction of the biphenyl groups, which results in enhanced stability of the cis isomers. Compound 1 is the first example of a structurally characterised mononuclear cis-bis(phosphanylthiolato)nickel(III) complex. Small amounts of the trinuclear complex [{PtI(1-P(Biph)-µ-2-S-C(6)H(4)-κ(2)S,P)}(3)] (4) are also formed besides the mononuclear platinum bis-chelate complex 3.

Theoretical study of structural patterns in CH2OP2 isomers.

DFT calculations have been performed on the derivatives of formula CH2OP2 to determine their total energy, the relative energy between the isomers and their geometry. Among compounds with a P-C-P linkage, the most stable one is the 2-hydroxy-1,2-diphosphirene II.1, a three-membered heterocycle with a P=C unsaturation. The phosphavinylidene(oxo)phosphorane HP=C=P(O)H IV.5 (which has the same skeleton as the experimentally obtained Mes*P=C=P(O)Mes*) lies 36.30 kcal mol⁻¹ above it. The least stable compounds are carbenes; the singlet carbenes are more stable than the triplet ones.

Computational investigation of the histidine ammonia-lyase reaction: a modified loop conformation and the role of the zinc(II) ion.

Possible reaction intermediates of the histidine ammonia-lyase (HAL) reaction were investigated within the tightly closed active site of HAL from Pseudomonas putida (PpHAL). The closed structure of PpHAL was derived from the crystal structure of PpHAL inhibited with L-cysteine, in which the 39-80 loop including the catalytically essential Tyr53 was replaced. This modified loop with closed conformation was modeled using the structure of phenylalanine ammonia-lyase from Anabaena variabilis (AvPAL) with a tightly closed active site as a template. Three hypothetical structures of the covalently bound intermediate in the PpHAL active site were investigated by conformational analysis. The distances between the acidic pro-S ß-hydrogen of the ligand and the appropriate oxygen atoms of Tyr53, Ty280 and Glu414--which may act as enzymic bases--in the conformations of the three hypothetical intermediate structures were analyzed together with the substrate and product arrangements. The calculations indicated that the most plausible HAL reaction pathway involves the N-MIO intermediate structure in which the L-histidine substrate is covalently bound to the N-3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) prosthetic group of the apoenzyme via the amino group. Density functional theory (DFT) calculations--on a truncated model of the N-MIO intermediate containing a Zn²âº ion coordinated to the imidazole ring of the ligand and to His83, Met382 and a water molecule--indicated that Zn-complex formation plays a role in the reactivity and substrate specificity of HAL.

Butterfly and rhombus structures for binuclear cobalt carbonyl sulfur and phosphinidene complexes of the type Co2(CO)6E2 (E = S, PX).

Theoretical studies on Co(2)(CO)(6)(PX)(2) derivatives (X = H, Cl, OH, OMe, NH(2), NMe(2)) predict the lowest energy structures to be butterfly structures containing five two-electron two-center bonds in the central Co(2)P(2) unit. Among these butterfly structures the energy increases as the unique bond forming the "body" of the butterfly changes from Co-Co to Co-P and then P-P. Higher energy rhombus structures are also found for Co(2)(CO)(6)(PX)(2) with only Co-P bonds in the Co(2)P(2) framework without any Co-Co or P-P bonds. In addition, for Co(2)(CO)(6)(POR)(2) (R = H, Me) still higher energy "diphosphine" structures are also found containing only three rather than four Co-P bonds, one P-P bond, and no Co...Co bond. For the isoelectronic Co(2)(CO)(6)S(2) a rhombus structure is competitive in energy with the butterfly structures with five structures lying within approximately 4 kcal/mol thereby predicting a fluxional system. A tetrahedrane structure was not found for Co(2)(CO)(6)S(2) in contrast to the tetrahedrane structure known experimentally for the related Fe(2)(CO)(6)S(2) with one less electron per metal atom.

From closo to isocloso structures and beyond in cobaltaboranes with 9 to 12 vertices.

Density functional theory (DFT) studies predict the dianions CpCoB(n-1)H(n-1)(2-) (n = 9, 10, 11, 12; Cp = eta(5)-C(5)H(5)) to have structures based on the most spherical deltahedra found in the isoelectronic boranes B(n)H(n)(2-). In the CpCoB(8)H(8)(2-) dianion the non-equivalent structures with the cobalt atom at a degree 4 vertex and at a degree 5 vertex are essentially degenerate in terms of energy (within approximately 1 kcal/mol). For the CpCoB(n-1)H(n-1)(2-) dianions (n = 10, 11, 12) the cobalt atom prefers energetically the vertices of the lowest possible degree (four for n = 10 and 11, five for n = 12). Structures for the neutral species CpCoB(n-1)H(n-1) (n = 10, 11, 12) based on isocloso deltahedra with the cobalt atom at a degree 6 vertex are preferred energetically by 9, 19, and 53 kcal/mol, respectively, over alternative structures. However, for CpCoB(8)H(8) the closo tricapped trigonal prismatic structure with the cobalt atom at a degree 5 vertex is energetically preferred by approximately 9 kcal/mol over the isocloso deltahedral structure with the cobalt atom at a degree 6 vertex. The lowest energy structures predicted for the dications CpCoB(8)H(8)(2+) and CpCoB(9)H(9)(2+) are highly oblate (flattened) deltahedra with the cobalt atom at a degree 7 vertex. A complicated potential energy surface was found for CpCoB(10)H(10)(2+) including non-deltahedral structures with a single quadrilateral or pentagonal face. The predicted lowest energy structures for both CpCoB(11)H(11) and CpCoB(11)H(11)(2+) are based on the same 12-vertex deltahedron with three degree 6, six degree 5, and three degree 4 vertices, and thus topologically different from the regular icosahedron normally found in boron chemistry.

Kinetic versus thermodynamic isomers of the deltahedral cobaltadicarbaboranes.

Synthesis of the deltahedral cobaltadicarbaboranes CpCoC(2)B(n-3)H(n-1) (n = 9, 10, 11, 12) typically leads initially to kinetically stable isomers with energies up to approximately 20 kcal/mol above the lowest energy isomers. Pyrolyses of these originally produced isomers typically results in isomerization to give more thermodynamically stable isomers. In this connection the relative stabilities of the CpCoC(2)B(n-3)H(n-1) (n = 9, 10, 11, 12) isomers have been investigated using density functional theory. For CpCoC(2)B(n-3)H(n-1) (n = 9, 10, 11) the isomers with both carbon atoms at degree 4 vertices are predicted to have the lowest energies. For CpCoC(2)B(9)H(11) the icosahedron is by far the preferred polyhedron. Among the nine possible icosahedral CpCoC(2)B(9)H(11) isomers, the unique isomer with the carbon atoms in antipodal (para) positions is the global minimum. However, the four CpCoC(2)B(9)H(11) isomers with the two carbon atoms in mutual non-antipodal non-adjacent (meta) positions lie within approximately 5 kcal/mol of the global minimum. These theoretical results are in reasonable agreement with the extensive experimental work on pyrolysis of CpCoC(2)B(n-3)H(n-1) (n = 9, 10, 11, 12) derivatives, mainly in the group of Hawthorne and co-workers during the 1970s.

(Diethyl-enetriamine)bis-(theophyllinato)zinc(II) dihydrate.

In the title compound, [Zn(C(7)H(7)N(4)O(2))(2)(C(4)H(13)N(3))]·2H(2)O, the Zn(II) ion is penta-coordinated by three N atoms of the diethyl-enetriamine ligand and one N atom of each of the two theophyllinate anions in a distorted trigonal-bipyramidal geometry. The Zn-N distances range from 2.076 (3) to 2.221 (3) Å. The crystal packing is stabilized by O-H⋯O, O-H⋯N and N-H⋯O hydrogen bonds involving the theophylline and diethyl-enetriamine ligands and uncoordinated water mol-ecules.

When arsine makes the difference: chelating phosphino and bridging arsinoarylthiolato gallium complexes.

The (organo)gallium compounds GaCl{(SC6H4-2-PPh2)-kappa2S,P}2 (1), Ga{(SC6H4-2-PPh2)-kappa2S,P}{(SC6H4-2-PPh2)-kappaS}2 (2), GaMe2{(SC6H4-2-PPh2)-kappa2S,P} (3), GatBu2{(SC6H4-2-PPh2)-kappa2S,P} (4), GatBu{(SC6H4-2-PPh2)-kappa2S,P}{(SC6H4-2-PPh2)-kappaS} (5), [GaMe2{(mu2-SC6H4-2-AsPh2)-kappaS}]2 (6), and GatBu{(SC6H4-2-AsPh2)-kappa2S,As}{(SC6H4-2-AsPh2)-kappaS} (7) were obtained from the reaction of 2-EPh2C6H4SH (E = P (PSH), As (AsSH)) with GaCl3 (1, 2) or GaR3 (R = Me, tBu; 3-7) in different molar ratios and under different reaction conditions. Compound 2 was also obtained from Li(PS) and GaCl3 (3.5:1). While a monomeric structure with a chelating phosphinoarylthiolato ligand is observed in GaMe2{(SC6H4-2-PPh2)-kappa2S,P} (3), a dimeric arsinoarylthiolato-bridged complex [GaMe2{(mu2-SC6H4-2-AsPh2)-kappaS}]2 (6) is obtained with the corresponding AsS- ligand. B3LYP/6-31G(d) calculations show that although the dimer is thermodynamically favored for both ligands, the formation of 3 is due to the combination of higher stability of the chelate compared with the monodentate phosphorus ligand and a higher barrier for the ring opening of the PS- than of the AsS- chelate.

Polyhedral structures with three-, four-, and five fold symmetry in metal-centered ten-vertex germanium clusters.

Studies using density functional theory (DFT) at the hybrid B3LYP level indicate that the relative energies of structures with three-fold, four-fold, and five-fold symmetry for centered 10-vertex bare germanium clusters of the general type M@Ge(10) (z) depend on the central metal atom M and the skeletal electron count. For M@Ge(10) clusters with 20 skeletal electrons the DFT results agree with experimental data on the isoelectronic centered 10-vertex bare metal clusters. Thus the lowest energy structure for Ni@Ge(10), isoelectronic with the known Ni@In(10) (10-), is a C(3v) polyhedron derived from the tetracapped trigonal prism. However, Zn@Ge(10) (2+) is isoelectronic with the known cluster Zn@In(10) (8-), which has the lowest energy structure, a D(4d) bicapped square antiprism. For the clusters Ni@Ge(10) (2-), Cu@Ge(10) (-), and Zn@Ge(10) that have 22 skeletal electrons the lowest energy structures are the D(4d) bicapped square antiprism predicted by the Wade-Mingos rules. For the clusters Ni@Ge(10) (4-), Cu@Ge(10) (3-), and Zn@Ge(10) (2-) that have 24 skeletal electrons the lowest energy structures are C(3v) polyhedra with 10 triangular faces and 3 quadrilateral faces derived from a tetracapped trigonal prism by extreme lengthening of the edges of the capped triangular face of the underlying trigonal prism. For the clusters Cu@Ge(10) (5-) and Zn@Ge(10) (4-) that have 26 skeletal electrons the lowest energy structures are the D(5d) pentagonal antiprisms predicted by the Wade-Mingos rules and the C(3v) tetracapped trigonal prism as a somewhat higher energy structure. However, for the isoelectronic Ni@Ge(10) (6-) the relative energies of these two structure types are reversed so that the C(3v) tetracapped trigonal prism becomes the global minimum. The effects of electron count on the geometries of the D(5d) pentagonal prism and D(4d) bicapped square antiprism centered metal cluster structures are consistent with the bonding/antibonding characteristics of the corresponding HOMO and LUMO frontier molecular orbitals.

PalladiumII and platinumII complexes with heteroditopic 10-(aryl)phenoxarsine (aryl = 2-C6H4OR, R = H, Me, Pr(i)) ligands: solvent-oriented crystallization of cis isomers.

The synthesis and characterization of 10-(o-alkoxyphenyl)phenoxarsines 2-ROC6H4As(C6H4)2O (R = H, Me, and Pri, As(C6H4)2O = phenoxarsine) and their platinum(II) and palladium(II) complexes cis-[PtCl2{2-PriOC6H4As(C6H4)2O-kappaAs}2] (1), trans-[PdCl2{2-PriOC6H4As(C6H4)2O-kappaAs}2] (2), cis-[PtCl2{2-HOC6H4As(C6H4)2O-kappaAs}2] (3), cis-[PdCl2{2-HOC6H4As(C6H4)2O-kappaAs}2] (4), cis-[PtI2{2-MeOC6H4As(C6H4)2O-kappaAs}2] (5), and trans-[PdCl2{2-MeOC6H4As(C6H4)2O-kappaAs}2] (6) are reported. The chelate complex cis-[Pt{2-OC6H4As(C6H4)2O-kappaAs,O}2] (7) is also described. The molecular structures of 1-4 and 7 were determined. The short As...O intramolecular interaction found in complexes 1-4 in the solid state was also verified by calculations at the B3LYP/LANL2DZ level for complex 2 and for 10-(o-isopropoxyphenyl)phenoxarsine in the gas phase, and this suggests that the interaction is a characteristic of the ligand rather than a packing effect. Calculations at the B3LYP/LANL2DZ and Oniom(B3LYP/LANL2DZ:uff) levels for complexes 1-4 showed that the solvent plays a crucial role in the crystallization (through geometry constraints) of the kinetically stable cis isomers.

Interplay among tetrahedrane, butterfly diradical, and planar rhombus structures in the chemistry of the binuclear iron carbonyl phosphinidene complexes Fe2(CO)6(PX)2.

Density functional theory studies on a series of Fe2(CO)6(PX)2 derivatives show the tetrahedrane to be the most stable for the alkyl (X = Me, tBu), P-H (X = H), and chloro (X = Cl) derivatives. However, butterfly diradical and planar rhombus structures are found to be more stable than tetrahedranes for the amino (X = NH2, NMe2, and NiPr2) and aryloxy (R = 2,6-tBu2-4-Me-C6H2O) derivatives. For the chloro (X = Cl) and methoxy (X = OMe) derivatives energetically accessible bishomotetrahedrane Fe2(CO)6P2(mu-X)2 isomers are observed in which the X substituents on the phosphorus atoms interact with the iron atom to form two direct Fe-X bonds at the expense of two of the four Fe-P bonds. In addition, the global minimum for the hydroxy (X = OH) derivative is an unusual FeP-butterfly structure with a central Fe-P bond as well as two external Fe-P bonds, one external P-P bond, and one external Fe=Fe double bond. Comparison of calculated with experimental nu(CO) frequencies shows that low-temperature Nujol matrix photolysis of (iPr2NP)2COFe2(CO)6 leads to a planar rhombus rather than a tetrahedrane isomer of Fe2(CO)6(PNiPr2)2.

1,3-Digermacyclobutanes with exocyclic C=P and C=P=S double bonds.

New 1,3-digermacyclobutanes, with two exocyclic C=PMes* bonds, and the corresponding first bis(methylenethioxo)phosphoranes with C=P(S)Mes* moieties have been synthesized.

Density functional theory study of twelve-atom germanium clusters: conflict between the Wade-Mingos rules and optimum vertex degrees.

Density functional theory (DFT) at the hybrid B3LYP level has been applied to Ge(12)(z) bare germanium clusters (z = -6, -4, -2, 0, +2, +4, +6) starting from 11 initial configurations. The Wade-Mingos rules are seen to have limited value in rationalizing the results since they frequently require vertex degrees higher than the optimum vertex degree of 4 for germanium. Thus the expected I(h) regular icosahedron is no longer the global minimum for Ge(12)(2-) although it remains a low energy structure for Ge(12)(2-) lying only 5.6 kcal mol(-1) above a bicapped arachno structure conforming to the Wade-Mingos rules. The three lowest energy structures for Ge(12)(4-) within 11 kcal mol(-1) are a prolate (elongated) polyhedron with six quadrilateral faces and eight triangular faces, the dual of the bisdisphenoid with four trapezoidal and four pentagonal faces, and a polyhedron with two quadrilateral and 16 triangular faces related but not identical to the polyhedron found in the known tetracarbon carboranes R(4)C(4)B(8)H(8). The lowest energy structures for the neutral Ge(12) are seen to be distorted versions of the icosahedron and the bicapped 10-vertex arachno lowest energy structures for Ge(12)(2-). The low energy structures for the even more hypoelectronic Ge(12)(2+) and Ge(12)(4+) are even more unusual including a hexacapped octahedron, a tetracapped square antiprism, and a double cube for Ge(12)(2+) and a C(2v) structure with a central unique degree 6 vertex for Ge(12)(4+).

Molecular rotors: design, synthesis, structural analysis, and silver complex of new [7.7]cyclophanes.

New molecular rotors, [7.7](2,6)pyridinocyclophanes (monomers and dimers) embedding 1,3-dioxanes in the bridges, were investigated by variable-temperature NMR, molecular modeling, and single-crystal X-ray diffractometry. The nitrogen-inside rotation of the pyridine ring is more hindered in the derivatives with longer distance between the bridges (i.e., para > meta and 2,6-pyridylene > ortho) and can be chemically stopped by complexation with CF(3)SO(3)Ag. [structure: see text]

Butterfly diradical intermediates in photochemical reactions of Fe2(CO)6(mu-S2).

Photolysis of the tetrahedrane Fe2(CO)6(mu-S2) at 450 +/- 35 nm in a Nujol matrix at low temperatures gives an isomer characterized by its nu(CO) infrared frequencies. Comparison of these experimental frequencies with those calculated by density functional theory using the BP86 functional indicates this photoisomer to be the butterfly singlet diradical Fe2(CO)6S2 isomer in which the S-S bond of the tetrahedrane is broken but the Fe-Fe bond is retained. Photolysis at higher energies (420-280 nm) results in CO loss from this singlet butterfly diradical as indicated again by comparison of the experimental infrared nu(CO) frequencies with those calculated for an Fe2(CO)5S2 isomer of this type.

Co-complexes of ortho-dilithiated thiophenol or 2-trimethylsilylthiophenol with lithiated TMEDA molecules: synthesis, crystal structures and theoretical studies (TMEDA = N,N,N',N'-tetramethylethylenediamine).

When an excess of nBuLi was used in the ortho-dilithiation of thiophenol or 2-trimethylsilylthiophenol in the presence of TMEDA (TMEDA = N,N,N',N'-tetramethylethylenediamine), deprotonation of TMEDA occurred and crystals of [Li3{(2-S-C6H4)(CH2MeNCH2CH2NMe2)(TMEDA)}]2 (1) or [Li4{(2-S-3-SiMe3-C6H3)(CH2MeNCH2CH2NMe2)2(TMEDA)}] (2) were obtained. Molecular orbital calculations on gas-phase 1 and 2 at the DFT B3LYP/6-31G(d) level reproduce the experimental structures fairly well. In spite of the short Li...Li distances, total electron density representations do not support the existence of Li...Li interactions.

DFT and the electromerism in complexes of iron with diatomic ligands.

A reliable procedure is proposed for assigning the electronic structures for large biologically-relevant systems, where the size of the model confines one to the use of density functional theory (DFT) methods, and where the risk of over-interpreting DFT-derived molecular orbitals and spin densities still exists. The proposed approach focuses on the use of the only DFT-derived parameter that is unanimously recognized to be reliable: the geometry. We examine DFT-derived O-O bond lengths in formally ferrous-dioxygen models, and compare them to bond lengths in free, non metal-bound, dioxygen, superoxide and peroxide moieties. Likewise, we compare the N-O bond lengths within ferrous-nitrosyl {FeNO}7 models, with the same parameter in free NO+, NO*, and HNO species. This allows a calibrated, straightforward way of assigning the electronic structure in systems where electromerism makes detailed single-reference molecular orbital analysis unreliable.

Periodic cages.

Various cages are constructed by using three types of caps: f-cap (derived from spherical fullerenes by deleting zones of various size), kf-cap (obtainable by cutting off the polar ring, of size k), and t-cap ("tubercule"-cap). Building ways are presented, some of them being possible isomerization routes in the real chemistry of fullerenes. Periodic cages with ((5,7)3) covering are modeled, and their constitutive typing enumeration is given. Spectral data revealed some electronic periodicity in fullerene clusters. Semiempirical and strain energy calculations complete their characterization.

Tin(IV) halide complexes of AsPh3) The structures of trans-SnCl4(AsPh3)2 and SnBr4(AsPh3).AsPh3.

The structures of two 1 : 2 adducts between tin(IV) halides and AsPh(3) have been determined. SnCl(4)(AsPh(3))(2) adopts a six-coordinate geometry at tin in which the two organoarsine donors are mutually trans. In contrast, SnBr(4)(AsPh(3))(2) is five-coordinate at tin and only one arsine is directly bonded to the metal, in an axial site of the trigonal bipyramid. The second AsPh(3) group has a close contact with the axially bound bromine [As...Br: 3.567(3) angstroms], which is a unique structural variation that depicts an intermediate in a halogen-transfer reaction between Group 14 and Group 15 elements. AACVD using SnCl(4)(AsPh(3))(2) generates a film containing SnO(2) and a second crystalline material which is possibly SnCl(2), but which contains no arsenic.