Mechanistic studies on the alcoholysis and aminolysis of [(MeZn)2{μ-N(H)tBu}{μ-N(CH2Py)2}]

The reaction of bis(2-pyridylmethyl)amine (II) with t-butylamine and dimethylzinc gives the heteroleptic [(MeZn)₂{μ-N(H)tBu}{μ-N(CH₂Py)₂}] (1). Stoichiometric alcoholysis of 1 with methanol leads to the exchange of the μ-N(H)tBu moiety. Almost quantitatively the corresponding methoxide [(MeZn)₂(μ-OMe){μ-N(CH₂Py)₂}] (2) is formed. Alternatively bis(alkylzinc)methoxide-bis(2-pyridylmethyl)amides (Alkyl = methyl (2), bis(trimethylsilyl)methyl) (3)) are also accessible by direct zincation of bis(2-pyridylmethyl)amine (II) and methanol with dialkylzinc regardless of the bulkiness of the alkyl groups. Extensive DFT calculations on the alcoholysis mechanism reveal the preferential insertion of methanol into a zinc amide bond rather than the cleavage of zinc carbon bonds. An intermediate with a Zn[μ-(MeO?H?NHR)]Zn functionality is predicted. Aminolyis of 1 with t-butylamine leads to intermediates with Zn[μ-(RNH ? H ? NHR)]Zn functionalities, respectively. We were able to detect the latter by ¹H NMR spectroscopy. The aminolysis of 1 with an excess of phenylamine results in a partial decomposition of the complex leading to the hexanuclear amide [{Zn(μ-N(H)Ph)}{MeZn(μ-N(H)Ph)}₂{μ-N(CH₂Py)₂}]₂ (4). Compound 2 is able to cleave silicon grease when dissolved in t-butylamine yielding [(MeZn)₂{μ-N(CH₂Py)₂}₂Zn{μ-(OMe₂Si)₂O}] (5). The X-ray structures of complexes 1-5 are discussed.     

Structural studies of bis(histidinato)nickel(II): Combined experimental and computational studies

A distorted octahedral nickel(II) complex, [Ni(2-amino-3-(1H-imidazol-4-yl)propanoic acid)₂] (1), has been synthesized by a solvothermal method and characterized by single-crystal X-ray diffraction. Geometry optimization in the gas phase and pyridine together with Hirshfeld surface and reduced density gradient analyses reveal that this complex shows different distortions from octahedral in the gas, liquid, and solid phases. The reason seems to be because of the presence of two intramolecular NH⋯O weak interactions in the gas phase and two sets of rather strong intermolecular NH⋯O and CH⋯O interactions in the solid phase. Time-dependent density functional theory (TD-DFT) calculations suggest that these different distortions result in different electronic absorption spectra.     

Structural and vibrational study on N-(biphenyl-2-thiocarbamoyl)-4-phenylcarboxamide

A new thiourea derivative, N-(biphenyl-2-thiocarbamoyl)-4-phenylcarboxamide, is synthesized and characterized by elemental analysis, FTIR, NMR and the single crystal X-ray diffraction study. The title compound crystallizes with two molecules in the asymmetric unit. The dihedral angle between the two aromatic rings in the biphenyl unit is 47.9(2) and 56.52(19)°, respectively, for the two molecules in the asymmetric unit. The molecular conformation is stabilized by intramolecular NH?O hydrogen bond. The crystal packing shows that the molecules form centrosymmetric dimers connected by NH?S hydrogen bonds. The vibrational properties have been studied by FTIR and FT-Raman spectroscopy along with quantum chemical calculations at the B3LYP/6-311 + G^* level of approximation. The main normal modes related with the thioamide bands are discussed.     

Docking studies to evaluate the biological activities of the Co(II) and Ni(II) complexes containing the triazine unit: supported by structural,spectral, and theoretical studies

Abstract

Two complexes of 5,6-di(2-furyl)-3-(2-pyridyl)-1,2,4-triazine (L), [Co(L)₂(NO₃)₂] (1), and [Ni(L)₂(NO₃)₂] (2), were prepared and identified along with L by elemental analysis, FT-IR, UV-Vis, and ¹H NMR spectroscopies and single-crystal X-ray diffraction. All coordination modes of the 1,2,4-triazine unit and also of the nitrato ligand in coordination with cobalt and nickel atoms were studied by analysis of the Cambridge Structural Database (CSD) to compare with the new results. X-ray structure analysis of complexes 1 and 2 revealed that the metal atom in both complexes has an octahedral geometry with MN₄O₂ environment (M: Co (1), Ni (2)). The ligand acts as a bidentate N^tzN^py-donor and forms a five-membered planar chelate ring. In addition to the hydrogen bonds, the crystal network is stabilized by π–π stacking interactions between pyridine rings of the ligands of adjacent complexes. The thermodynamic stability of the two conformational isomers of the 5,6-di(2-furyl)-3-(2-pyridyl)-1,2,4-triazine and their charge distribution patterns were studied by DFT and NBO analysis, respectively. The ability of the uncoordinated ligand conformers and complexes 1 and 2 to interact with nine selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, and Top II) was investigated by docking calculations and compared with that of doxorubicin. Also an analog of the ligand in which the furyl rings are replaced by phenyl groups is included in these studies.     

Spectroscopic and theoretical studies on axial coordination of bis(pyrrol-2-ylmethyleneamine)phenyl complexes

Metal (M=Zn(II), Ni(II), Cu(II)) complexes with tetradentate Schiff base ligand, bis(pyrrol-2-ylmethyleneamine)phenyl, has been synthesized and characterized by elemental analyses, (1)H NMR, mass spectra and UV-vis spectra. The standard association constants (K(theta)) and the thermodynamic parameters (Delta(r)H(m)(theta),Delta(r)S(m)(theta),Delta(r)G(m)(theta)) for axial coordination of imidazole derivatives with these Shiff base complexes were measured with UV-vis spectrophotometric titration. The decrease of enthalpy is found to be the drive of the axial coordination. Our Schiff base complexes can incorporate two axial ligands, except 2-Et-4-MeIm with two big substituents of great steric bulk according to stoichiometry of 1:1. ZnL displays high selectively binding to imidazole due to the steric bulk effect. Supporting density functional theory (DFT) calculations have been undertaken on B3LYP/6-31G(d) level.     

Structural conversion of an oxazolidine ligand upon treatment with copper(I) and (II) halides; structural,spectral, theoretical and docking studies

Abstract

In this work, the 2-(2-(pyridin-2-yl)oxazolidin-3-yl)ethanol (AEPC) ligand was prepared under solvent free conditions using ultrasonic irradiation, before reaction with a Cu(NO₃)₂/KSCN mixture, CuCl₂ and CuI, the products of which were characterized by elemental analysis, UV-Vis, FT-IR spectroscopy and single-crystal X-ray diffraction. The X-ray analyses results revealed that AEPC, after reactions with the three copper(I/II) halides, gave structures ([Cu(DEA)Cl₂] (2), DEA?=?diethanolamine, [Cu(BHEG)₂] (3), BHEG?=?bis(2-hydroxyethyl)glycinato); however, it retains its structure on treatment with Cu(NO₃)₂/KSCN mixture ([Cu(AEPC)(NCS)₂] (1)). The geometrical parameters for the complexes were compared with the Cambridge Structural Database (CSD) and coordination modes for thiocyanate ion were extracted. In the crystal structure of 1, the copper ion has a distorted square-pyramidal geometry and a CuN^pyN₂^NCSN^tertO^alc environment in which the AEPC acts as NN'O-donor in a facial coordination mode. In the crystal structure of 2, the copper ion has a Cu(N^sec)(O^alc)₂Cl₂ environment and distorted square-pyramidal geometry in which the DEA ligand is coordinated as a mer-NO₂-donor. The copper ion in 3 has a CuN₂O₄ environment and distorted octahedral geometry. The ability of these compounds to interact with the nine biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II) was investigated by Docking calculations and compared with that of doxorubicin. The thermodynamic stability of 1 and its isomer and also charge distribution patterns were studied by DFT and NBO analysis, respectively.     

Hydrosilylation, hydrocyanation, and hydroamination of ethene catalyzed by bis(hydrido-bridged)diplatinum complexes: Added insight and predictions from theory

Details on the reaction mechanism of the catalytic cycle of hydrosilylation, hydrocyanation and hydroamination of ethene catalyzed by bis(hydrido-bridged)diplatinum complexes were obtained with the aid of DFT by calculating the relevant intermediates and transition state structures. The catalytically “active” species identified are the 16e coordinatively unsaturated mononuclear [Pt(X)(H)(PH₃)(η²-C₂H₄)] (X = SiH₃, CN, NH₂) species formed upon addition of the ethene molecule on the monomeric [Pt(X)(H)(PH₃)] precursors. All crucial reaction steps encapsulated in the entire catalyzed courses have been scrutinized. The following three steps are found to be critical for these catalytic reactions: (i) the migration of the hydride to the acceptor C atom of the coordinated ethene substrate, (ii) the reductive elimination of the final product and (iii) the oxidative addition process that regenerates the catalyst with activation barriers of 13.1, 16.5 and 13.3 kcal/mol for hydrosilylation, 7.1, 31.0 and 2.8 kcal/mol for hydrocyanation and 11.7, 39.7 and 39.0 kcal/mol for hydroamination reactions. In all cases the rate-determining step is that of the reductive elimination of the final product having always the highest activation barrier. The overall catalytic processes are exergonic with the calculated exergonicities being −13.5 (−8.0), −16.1 (−10.4) and −38.8 (−46.7) kcal/mol for the hydrosilylation, hydrocyanation and hydroamination of ethene, respectively, at the B3LYP (CCSD(T)) levels of theory. According to energetic span of the cycle called δE, which determines the frequency of the catalytic cycle, we found that the catalytic efficiency of the hydrido-bridged diplatinum complexes follows the trend: hydrocyanation ≈ hydrosilylation > hydroamination.     

[Ga6R8]2– (R = SiPh2Me): Eine metalloide Clusterverbindung mit einem unerwarteten Ga6‐Gerüst

[Ga₆R₈]^2– (R = SiPh₂Me): A Metalloid Cluster Compound with an Unexpected Ga₆‐Frame The reaction of a metastable solution of GaBr with a solution of LiSiPh₂Me in a toluene/THF mixture results in orange coloured crystals of [Ga₆(SiPh₂Me)₈]^2– · 2 [Li(THF)₄]⁺ ( 1 ). The unexpected structure of the planar Ga₆ frame (C_2h) could also be realized with the help of DFT calculation. DFT calculations furthermore show that 1 is energetically favoured against an octahedral Ga₆R₆^2– species and R₂. In contrast calculations for the similar Al and B species show that in these cases the octahedral entities are favoured. These results demonstrate that even for similar compounds of B, Al, and Ga Wade rules are too general and that they cannot predict the correct structure. Moreover the atomic arrangement within 1 shows that a structure is preferred which is also present in allotropic β‐Ga and that therefore clusters of this type should be called metalloid or more general elementoid.     

Studies in werner clathrates. Part 2. Structures of bis (isothiocyanato) tetra (4-phenylpyridine) nickel (II)· 4-dimethylsulphoxide,bis (isothiocyanato) tetra (3-methylpyridine) nickel (II)· chloroform and bis (isothiocyanato) tetra (3,5-dimethylpyridine) nickel (II)

The structures of Ni(NCS)₂(4-PhPy)₄·4DMSO and Ni(NCS)₂(3-MePy)₄·CHCl₃ have been elucidated. Movement of guest molecules through channels in the host structure was simulated by potential energy calculations. Ni(NCS)₂(3,5-diMePy)₄ does not form inclusion compounds. An intra-molecular potential energy study shows that theortho-hydrogens on the 3,5-dimethylpyridine ligands control the conformation of the molecule. The same result is obtained with the 4-methylpyridine ligand, which suggests that the extent of rotation of substituted pyridines about the Ni–N bounds is not a factor governing clathrate formation. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82030 (43 pages).     

X-ray structure of [Re(NO)2.09Br1.91(PPh3)2] and DFT studies of [Re(NO)2Br2(PPh3)2]

The crystal and molecular structure of [Re(NO)_2.09Br_1.91(PPh₃)₂] and DFT studies of [Re(NO)₂Br₂(PPh₃)₂] are reported. The linearly bonded nitrosyl ligands adopt cis geometry, and two bulky triphenylphosphine molecules occupy axial positions of a distorted octahedral coordination sphere. The cis-nitrosyl grouping with respect to PPh₃ molecules (π-acid ligands) is the result of the electronic influence of the multiply bonded ligand, which forces the metal nonbonding d electrons to lie in the plane perpendicular to the M–NO bond axis.     

Coordination diversity in tin compounds with bis(benzoxazole)phenol as a polydentate ligand: Synthesis and crystal structure studies

Abstract

The reaction of 2,6-bis(benzoxazolyl)-4-tert-butylphenol (HL) with [ⁿBu_xSnCl_4?x] (x?=?0, 1) in 1:1 stoichiometry yielded the tin coordination complexes [(HL)SnⁿBu_xCl_4?x] [x?=?0 (1); x?=?1 (2)]. Deprotonation of HL was performed using reagents having groups with high basicity such as ⁿBuLi or [Sn{N(SiMe₃)₂}₂]. These basic reagents prompted the coordination of the ligand in its anionic form, yielding the complexes [(thf)₂Li(L)SnCl₄] (3) and [(L)Sn{N(SiMe₃)₂}] (4), respectively. The molecular structure of HL displayed an intramolecular hydrogen bond OH—N and a planar arrangement of the bis(benzoxazolyl)phenolic system. In the molecular structures of both complexes containing HL an intramolecular hydrogen bond of NH—O type was also present. The coordination of the ligand in either neutral or anionic form is described by a κO,κN chelate mode toward Sn. All complexes displayed bis(benzoxazolyl)phenolic moieties close to planar; the least planar system was observed in 4 that was also studied by DFT methods.     

Electronic Structure and Hydrogen Bonding in a Dicobalt(III) Werner Complex

The bonding of the O-O group in the dicobalt cation 1a [(NH₃)₆Co₂(μ-O₂)(μ-OH)(μ-NH₂)]³⁺ was studied by DFT methods (ADF program) and the bridging O₂ ligand was characterized as superoxide(O₂⁻). In this complex, three bridging ligands connect the two cobalt atoms, forcing a cis conformation of the Co-O-O-Co atoms. A comparison was made with [(NH₃)₁₀Co₂(μ-O₂)]⁵⁺, 2a, where a trans arrangement is observed. Superoxide binds more strongly to the dicobalt(III) fragment in 2a than in 1a, both as a result of weaker Pauli repulsion and stronger covalent interaction. It was found that in 1a the electronic structure with one unpaired electron, where cobalt is formally Co(III), d⁶, and O₂ carries one negative charge gives rise to the most stable structure, compared to possibilities with three and five unpaired electrons. The hydrogen bonds in the crystal were analyzed and the interactions between one water molecule or one nitrate ion studied in more detail.     

Structures of Mn(II) complexes of bis(2-pyridylmethyl)amine (bpa) and (2-pyridylmethyl)(6-methyl-2-pyridylmethyl)amine (Mebpa): geometric isomerism in the solid state

The crystal structures of [Mn(bpa)₂](ClO₄)₂ (1), [bpa?=?bis(2-pyridylmethyl)amine], and Mn(6-Mebpa)₂(ClO₄)₂ (2), [6-Mebpa?=?(6-methyl-2-pyridylmethyl)(2-pyridylmethyl)amine] have been determined. In 1, two facial [Mn(bpa)₂]²⁺ isomers are observed in the same unit cell, one with C _i (1a) and the other with C₂ (1b) symmetries. In 2, only the isomer with C₂ symmetry is observed. The structure of [Mn(bpa)₂]²⁺ with only C₂ symmetry has been reported previously (Inorg. Chem., 31, 4611 (1992)). The bond length order Mn–N_amine?>?Mn–N_pyridyl, observed in the C₂ and the C _i isomers in the crystals of 1, is the reverse of the order observed in the structure of [Mn(bpa)₂](ClO₄)₂ which contains only the C₂ isomer in the unit cell. The structure of 2 in which only the C₂ isomer is found, also shows the bond length order Mn–N_pyridyl?>?Mn–N_amine. In cyclic voltammetric experiments in acetonitrile solutions, 1 and 2 show irreversible anodic peaks at E _p?=?1.60 and 1.90?V respectively, (vs. Ag/AgCl), assigned to the oxidation of Mn(II) to Mn(III). The substantially higher oxidation potential of 2 is attributable to a higher rearrangement energy in complex 2 due to the steric effect of the methyl substituent.     

Etude théorique par la méthode DFT des structures non-classiques des systèmes X2H2F2 (X=Si, Ge, Sn)

The structure and the relative stability of isomers of molecules X₂H₂F₂ (X=Si, Ge, Sn) have been studied using the density functional theory (DFT). We have determined the optimised structures of the substituted isomers. The XX bond have been studied and compared to that of the parent molecules: X₂H₄. It appears that, for the planar and trans ethylenic systems, the double bond character of the XX decreases when the hydrogen atoms are substituted by fluorine atoms. The most stable structure is shown to be the one where the two fluorine atoms are fixed on the same atom. The bridged structures are also studied.     

Cobalt Chalcogenide Clusters. Synthesis,Characterization and DFT Calculations of [Co4Se2(CO)10] and [Co4Te2(CO)11]. Crystal Structure of [Co8Se4(CO)16(μ‐dppa)2]

The reactions of [Co₂(CO)₈] with E(SiMe₃)₂ (E = Se, Te) in CH₂Cl₂ result in the formation of the compounds [Co₄Se₂(CO)₁₀]> ( 1 ) and [Co₄Te₂(CO)₁₁] ( 2 ), respectively. Both cluster complexes have similar molecular structures in which the cobalt atoms form four‐membered rings with μ₄‐bridging chalcogen atoms (Se and Te) above and below the plane of the metal atoms and the carbonyl ligands as either terminal or μ₂‐bridging ligands. DFT‐calculations for both compounds have been carried out in order to obtain some more information about their electronic distribution. In the presence of the phosphine Ph₂PC≡CPPh₂ (dppa), the reaction of [Co₂(CO)₈] with Se(SiMe₃)₂ leads to the formation of [Co₈Se₄(CO)₁₆(μ‐dppa)₂] ( 3 ). During the reaction two molecules of [Co₂(CO)₈] have been added to the acetylene groups of the dppa ligands, whilst the remaining cobalt atoms coordinate to the phosphorus atoms of the phosphine. In this compounds the selenium atoms act as μ₃‐ligands, bridging the metal atoms bonded to the phosphorus with those bonded to the acetylene groups.     

Half-sandwich ruthenium(II)-arene complexes: synthesis,spectroscopic studies,biological properties,and molecular modeling

In search for antitumor metal-based drugs that would mitigate the severe side-effects of cisplatin, Ru(II) complexes are gaining increasing recent interest. In this work, we report on the synthesis, characterization (¹H- and ¹³C-NMR, FT-IR), and cytotoxicity studies of two new half-sandwich organometallic Ru(II) complexes of the general formula [Ru(η⁶-arene)(XY)Cl](PF₆) where arene?=?benzene or toluene and XY?=?bidentates: dipyrido[3,2-a:2′,3′-c]phenazine (dppz) or 2-(9-anthryl)-1H-imidazo[4,5-f][1,10]phenanthroline (aip), which are bound to Ru(II) via two phenanthroline-N atoms in a characteristic “piano-stool” configuration of Ru(II)-arene complexes—as confirmed by vibrational and NMR spectra. In addition, cytotoxic studies were performed for similar half-sandwich organometallic [Ru(η⁶-p-cymene)(Me₂dppz)Cl]PF₆ complex (Me₂dppz = 11,12-dimethyl-dipyrido[3,2-a:2′,3′-c]phenazine). This study is complemented with elaborate modeling with density functional theory (DFT) calculations, which provided insight into reactive sites of Ru(II) structures, further detailed by molecular docking on the B-DNA dodecamer, which identified binding sites and affinities: most pronounced for the [Ru(η⁶-benzene)(aip)Cl](PF₆) in both A-T and G-C regions of the DNA minor groove. Cytotoxic activity was probed versus tumor cell lines B16, C6, and U251 (B16 mouse melanoma, C6 rat glioma, U251 human glioblastoma) and non-tumor cell line HACAT (HACAT normal human keratinocytes).     

X-ray diffraction studies of two azametallatranes. Peculiarities of structures of N,N′,N″-tris(trimethylsilyl)azametallatranes using DFT calculations

Single crystal structures of N(CH₂CH₂NSiMe₃)₃Si-Vinyl (1) and N(CH₂CH₂NSiMe₃)₃Si-n-Butyl (2) were determined by X-ray diffraction studies: both compounds show weak transannular N_ax→M interactions (1, d(N_ax→Si)=2.712(1) Å, 2, d(N_ax→Ge)=2.743(3) Å). General trends for molecular structures of the group 14 elements (Si, Ge, Sn) azametallatranes are discussed with also included DFT calculations data.     

Structure of the Ligated Ag60 Nanoparticle [{Cl@Ag12}@Ag48(dppm)12] (where dppm=bis(diphenylphosphino)methane)

A novel bisphosphine ligated Ag₆₀ nanocluster, [{Cl@Ag₁₂}@Ag₄₈(dppm)₁₂], has been dis-covered and characterized by X-ray crystallography. It consists of a central chloride located inside an icosahedral silver core layer, which is further encased by a second shell of 48 silver atoms/ions, which are capped with 12 bis(diphenylphosphino)methane (dppm) ligands. Due to lack of sufficient material the cluster could not be further characterized by other methods. DFT calculations were carried out on the cation [{Cl@Ag₁₂}@Ag₄₈(dppm)₁₂]⁺ to determine if it corresponds to a superatom with a core count of n=58. The DFT optimized structure is in agreement with X-ray ndings, but the low value of the HOMO-LUMO gap does not support superatom stability.