Synthesis and coordination chemistry of 2-(di-2-pyridylamino)pyrimidine; structural aspects of spin crossover in an Fe(II) complex

This paper was accepted on February 26 20122-(Di-2-pyridylamino)pyrimidine (L), a potentially ditopic tetradentate ligand, was synthesized from commercially available di-2-pyridylamine and 2-chloropyrimidine. Despite being capable of bridging two metal atoms with bidentate chelation of both metal centres, L prefers to chelate or bridge through the more basic pyridyl donors of the di-2-pyridylamine moiety. Mononuclear trans-[Fe(NCS)2(L)2] and [Cu(L)2(H2O)](BF4)2•H2O complexes, and a discrete [Ag2(L)4](PF6)2 metallomacrocycle were isolated and structurally characterized by X-ray crystallography. A mononuclear palladium complex [PdCl2(L)]•(solvate), where solvate = ½H2O or CH2Cl2, was also readily obtained in 71% yield. One example of the ligand acting as a bis(bidentate) bridging ligand was observed in a dinuclear [(PdCl2)2(L)]•¾H2O complex that was obtained only in very low yield (ca. 3%) from the reaction that produced [PdCl2(L)]•½H2O. trans-[Fe(NCS)2(L)2] undergoes a temperature dependent HS-LS (HS = high spin; LS = low spin) crossover at ca. 205 K that was 2 observed by X-ray crystallography and magnetic measurements and attempts were made to understand the structural basis of this process. Despite efforts to isolate examples of L bridging two iron(II) centres, only the mononuclear trans-[Fe(NCS)2(L)2] species could be obtained.Rachel S. Crees, Boujemma Moubaraki, Keith S. Murray, and Christopher J. Sumb

Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding

Inner-sphere complexation of cations at the rutile-water interface: A concise surface structural interpretation with the CD and MUSIC model

Acid–base reactivity and ion-interaction between mineral surfaces and aqueous solutions is most frequently investigated at the macroscopic scale as a function of pH. Experimental data are then rationalized by a variety of surface complexation models. These models are thermodynamically based which in principle does not require a molecular picture. The models are typically calibrated to relatively simple solid-electrolyte solution pairs and may provide poor descriptions of complex multi-component mineral–aqueous solutions, including those found in natural environments. Surface complexation models may be improved by incorporating molecular-scale surface structural information to constrain the modeling efforts. Here, we apply a concise, molecularly-constrained surface complexation model to a diverse suite of surface titration data for rutile and thereby begin to address the complexity of multi-component systems. Primary surface charging curves in NaCl, KCl, and RbCl electrolyte media were fit simultaneously using a charge distribution (CD) and multisite complexation (MUSIC) model [Hiemstra T. and Van Riemsdijk W. H. (1996) A surface structural approach to ion adsorption: the charge distribution (CD) model. J. Colloid Interf. Sci. 179, 488–508], coupled with a Basic Stern layer description of the electric double layer. In addition, data for the specific interaction of Ca2+ and Sr2+ with rutile, in NaCl and RbCl media, were modeled. In recent developments, spectroscopy, quantum calculations, and molecular simulations have shown that electrolyte and divalent cations are principally adsorbed in various inner-sphere configurations on the rutile 1 1 0 surface [Zhang Z., Fenter P., Cheng L., Sturchio N. C., Bedzyk M. J., Predota M., Bandura A., Kubicki J., Lvov S. N., Cummings P. T., Chialvo A. A., Ridley M. K., Bénézeth P., Anovitz L., Palmer D. A., Machesky M. L. and Wesolowski D. J. (2004) Ion adsorption at the rutile–water interface: linking molecular and macroscopic properties. Langmuir 20, 4954–4969]. Our CD modeling results are consistent with these adsorbed configurations provided adsorbed cation charge is allowed to be distributed between the surface (0-plane) and Stern plane (1-plane). Additionally, a complete description of our titration data required inclusion of outer-sphere binding, principally for Cl- which was common to all solutions, but also for Rb+ and K+. These outer-sphere species were treated as point charges positioned at the Stern layer, and hence determined the Stern layer capacitance value. The modeling results demonstrate that a multi-component suite of experimental data can be successfully rationalized within a CD and MUSIC model using a Stern-based description of the EDL. Furthermore, the fitted CD values of the various inner-sphere complexes of the mono- and divalent ions can be linked to the microscopic structure of the surface complexes and other data found by spectroscopy as well as molecular dynamics (MD). For the Na+ ion, the fitted CD value points to the presence of bidenate inner-sphere complexation as suggested by a recent MD study. Moreover, its MD dominance quantitatively agrees with the CD model prediction. For Rb+, the presence of a tetradentate complex, as found by spectroscopy, agreed well with the fitted CD and its predicted presence was quantitatively in very good agreement with the amount found by spectroscopy

Aquachlorido(2-{[6-(dimethylamino)pyrimidin-4- yl]sulfanyl}pyrimidine-4,6-diamine)copper(II) chloride hydrate

A copper(II) complex of the non-symmetric bidentate ligand 2-{[6-(di­methyl­amino)­pyrimidin-4-yl]sulfan­yl}pyrimidine-4,6-di­amine (L1) is reported. The single-crystal X-ray structure of aqua­[aqua/chlorido­(0.49/0.51)](2-{[6-(di­methyl­amino)­pyrimidin-4-yl]sulfan­yl}pyrimidine-4,6-di­amine)­copper(II) 0.49-chloride 1.51-hydrate, [CuCl1.51(C10H13N7S)(H2O)1.49]Cl0.49·1.51H2O or [(L1)Cl1.51(H2O)1.49Cu]0.49Cl·1.51H2O, exhibits distorted square-pyramidal geometry around the metal centre, with disorder in the axial position, occupied by chloride or water. The six-membered metal–chelate ring is in a boat conformation, and short inter­molecular S- - -S inter­actions are observed. In addition to its capacity for bidentate metal coordination, the ligand has the ability to engage in further supra­molecular inter­actions as both a hydrogen-bond donor and acceptor, and multiple inter­actions with lattice solvent water mol­ecules are present in the reported structure

Range separated hybrid density functional study of organic dye sensitizers on anatase TiO2_2 nanowires

The adsorption of organic molecules coumarin and the donor-$\pi$-acceptor type tetrahydroquinoline (C2-1) on anatase (101) and (001) nanowires have been investigated using screened Coulomb hybrid density functional theory calculations. While coumarin forms single bond with the nanowire surface, C2-1 additionally exhibits bidentate mode giving rise to much stronger adsorption energies. Nonlinear solvation effects on the binding characteristics of the dye chromophores on the nanowire facets have also been examined. These two dye sensitizers show different electronic charge distributions for the highest occupied and the lowest unoccupied molecular states. We studied the electronic structures in terms of the positions of the band edges and adsorbate related band gap states and their effect on the absorption spectra of the dye-nanowire combined systems. These findings were interpreted and discussed from the view point of better light harvesting and charge separation as well as in relation to more efficient charge carrier injection into the semiconductor nanowire.Comment: 8 pages, 4 figures, and 1 tabl

Insights Into the Carboxyltransferase Reaction of Pyruvate Carboxylase From the Structures of Bound Product and Intermediate Analogs

Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we report three X-ray crystal structures of the Rhizobium etli PC CT domain with the bound inhibitors oxalate, 3-hydroxypyruvate, and 3-bromopyruvate. Oxalate, a stereoelectronic mimic of the enolpyruvate intermediate, does not interact directly with the metal ion. Instead, oxalate is buried in a pocket formed by several positively charged amino acid residues and the metal ion. Furthermore, both 3-hydroxypyruvate and 3-bromopyruvate, analogs of the reaction product oxaloacetate, bind in an identical manner to oxalate suggesting that the substrate maintains its orientation in the active site throughout catalysis. Together, these structures indicate that the substrates, products and intermediates in the PC-catalyzed reaction are not oriented in the active site as previously assumed. The absence of a bidentate interaction with the active site metal appears to be a unique mechanistic feature among the small group of biotin-dependent enzymes that act on α-keto acid substrates

Anatase TiO2_2 Nanowires Functionalized by Organic Sensitizers for Solar Cells : A Screened Coulomb Hybrid Density Functional Study

The adsorption of two different organic molecules cyanidin glucoside (C$_{21}$O$_{11}$H$_{20}$) and TA-St-CA on anatase (101) and (001) nanowires have been investigated using the standard and the range separated hybrid density functional theory calculations. The electronic structures and optical spectra of resulting dye--nanowire combined systems show distinct features for these types of photochromophores. The lowest unoccupied molecular orbital of the natural dye cyanidin glucoside is located below the conduction band of the semiconductor while, in the case of TA-St-CA, it resonates with the states inside the conduction band. The wide-bandgap anatase nanowires can be functionalized for solar cells through electron-hole generation and subsequent charge injection by these dye sensitizers. The intermolecular charge transfer character of Donor-$\pi$-Acceptor type dye TA-St-CA is substantially modified by its adsorption on TiO$_2$ surfaces. Cyanidin glucoside exhibits relatively stronger anchoring on the nanowires through its hydroxyl groups. The atomic structures of dye--nanowire systems re-optimized with the inclusion of nonlinear solvation effects showed that the binding strengths of both dyes remain moderate even in ionic solutions.Comment: 11 pages, 6 figure

Bidentate N,O-prolinate ruthenium benzylidene catalyst highly active in RCM of disubstituted dienes

The synthesis of a bidentate N,O-prolinate ruthenium benzylidene from commercially available starting materials and its activity in ring-closing metathesis of functionalized disubstituted dienes at 30 °C is disclosed

Synthesis of Solution-Phase Phosphoramidite and Phosphite Ligand Libraries and Their In Situ Screening in the Rhodium-Catalyzed Asymmetric Addition of Arylboronic Acids

Herein, we report the automated parallel synthesis of solution-phase libraries of phosphoramidite ligands for the development of enantioselective catalysts. The ligand libraries are screened in situ in the asymmetric rhodium-catalyzed addition of arylboronic acids to aldehydes and imines. It is shown that the described methodology results in the straightforward discovery of leads for highly efficient enantioselective catalysts.

Influence of C6_{6}H4_{4}(OH)2_{2} isomers on water disinfection by photocatalysis: a computational study

Solar disinfection by photocatalysis is one of the promising methods used for drinking water disinfection. It leads to the destruction of bacteria like $Escherichia$ $Coli$ ($E.$ $Coli$). In this paper, we compare our theoretical results with experimental ones done previously by A.G. Rinc\'on and his colleagues concerning the order of decay of C$_{6}$H$_{4}$(OH)$_{2}$ isomers in the presence of titanium dioxide TiO$_{2}$, and show the influence of optical properties of those molecules on $E.$ $Coli$ inactivation. According to the adsorption energy parameter, we find that catechol has the highest adsorption degree on titanium dioxide, followed by resorcinol, and finally hydroquinone. Three dihydroxybenzene isomers absorb photons belonging to ultraviolet (UV) range. The lowest absorption energies of resorcinol, catechol and hydroquinone are respectively 3.42, 4.44 and 4.49 eV.Comment: 7 pages, 3 figures, 1 tabl