Synthesis and characterization of a family of binuclear non-heme iron monooxygenase model compounds: Evidence for a “phenolate/amide carbonyl (PAC) shift” upon oxidation

A series of binuclear iron compounds has been synthesized using diamide, bis-phenolate ligands in which the carbon-linker between the amide nitrogen atoms has been varied. Two diferrous compounds in the series, along with their two-electron oxidized, di-μ-methoxy-bridged counterparts, have been crystallographically characterized, as have the di-μ-methoxy compounds (H₂Hbab = 1,2-bis(2-hydroxybenzamido) benzene, H₂Hbach = trans-1,2-bis(2-hydroxybenzamido) cyclohexane, H₂Hbame = 1,2-bis(2-hydroxybenzamido) ethane, H₂Hbap = 1,3-bis(2-hydroxybenzamido) propane, H₂Hbabn = 1,4-bis(2-hydroxybenzamido) butane, H₂Hbapen = 1,5-bis(2-hydroxybenzamido) pentane, N-MeIM = N-methylimidazole and OMe = methoxide). are structurally very similar to previously reported diferrous compounds of this family of ligands that have been shown to be active as oxygen atom transfer catalysts. Flexibility in the carbon-linker allows some variability in the orientation of the phenolate arms of the ligands in the diferric di-μ-methoxy compounds, but the Fe₂O₂ core remains largely unchanged across the series. Two-electron oxidation of the ferrous compounds in methanol shows a substantial ligand rearrangement that is consistent with other spectroscopic, electrochemical and kinetic investigations. The loss of both phenolate bridges upon oxidation is reminiscent of the “carboxylate shift” observed in binuclear non-heme enzymes and could provide insight into the driving force behind this family of compounds’ function as a catalyst.     

A joint computational and experimental study of a novel dioxomolybdenum(VI) complex bearing chiral N,N-dimethyllactamide ligand

A new cis-dioxomolybdenum complex MoO₂(DMLA)₂ (DMLA = N,N-dimethyllactamide) has been synthesized and characterized by X-ray crystallography, H NMR and IR spectroscopies and electronic structure calculations at DFT/B3LYP level. This compound (chemical formula C₁₀H₂₀MoO₆N₂) crystallizes in the orthorhombic space group P2₁2₁2₁ with Z = 4, a = 6.9357(2) ?, b = 11.8761(4) ?, c = 17.7251(5), V = 1460.00(8) ?³ and renders a slightly distorted octahedral structure with two long Mo-O bonds (2.253(3) ? and 2.257(3) ?) trans to each of the MoO groups and with two short Mo-O bonds of 1.942(3)4 ? cis to them. The MoO bond length are 1.715(3) and 1.704(3) ?). Each lactamide ligand is bidentate; they are coordinated in their deprotonated form with the carbonyl oxygen occupying a position trans to the MoO moiety while the deprotonated hydroxyl oxygen is located cis to them. Structural characterization is complemented by DFT/B3LYP calculations.     

Calculation of lipophilicity for Pt(II) complexes: experimental comparison of several methods

Platinum containing compounds are promising antitumor agents, but must enter cells before reaching their main biological target, namely DNA. Their distribution within the body, and hence their activity is to a large extent determined by their lipophilicity, thus there is a strong interest to develop computational methods to predict this important property. This study analyses accuracy of five methods, namely ALOGPS, KOWWIN, CLOGP and two quantum chemical approaches, to predict octanol/water partition coefficients (log P) for sets of 43 and 12 Pt(II) complexes, collected from the literature and measured by the authors, respectively. All methods gave generally poor results with mean absolute error (MAE) of between 0.8 and 3 log units for prediction of new compounds. Extension of the ALOGPS program with data from the literature set resulted in the best prediction ability, MAE = 0.46, for the measured molecules. The program was also able to correctly predict errors in calculated log P values. It is freely available for interactive use at http://www.vcclab.org.     

Synthesis of bimetallic fulvalene and bis(cyclopentadienyl)methane derivatives of niobium and tantalum tetracarbonyl

Ring coupled bimetallic derivatives (μ-η^5:5-C₅H₄C₅H₄)[Nb(CO)₄]₂ and [μ-CH₂(η⁵-C₅H₄)₂][M(CO)₄]₂, where M = Nb and Ta have been prepared. The molecular structures of the latter two compounds have been determined: , triclinic, , a = 8.028(2) Å, b = 11.414(1) Å, c = 12.711(2) Å, α = 75.020(8)°, β = 80.34(2)°, γ = 79.46(2)°, V = 1097.3(4) ų, Z = 2, R(F) = 2.79%; [μ-CH₂(η⁵-C₅H₄)₂][Ta(CO)₄]₂, triclinic, , a = 7.815(3) Å, b = 10.275(4) Å, c = 13.135(4) Å, α = 104.25(3)°, β = 100.26(4)°, γ = 96.86(3)°, V = 991.2(6) ų, Z = 2, R(F) = 3.00%.     

The aluminium(III)-sialic acid interaction: A potential role in aluminium-induced cellular membrane degeneration

The coordination between Al(III) and sialic acid (N-acetylneuraminic acid, HL, pK_a = 2.58 ± 0.01) was studied by potentiometric titrations at 25 °C in aqueous 0.2 M KCl, by ¹H NMR, and by electrospray ionization mass spectrometry (ESI-MS). The potentiometric measurements gave the following aluminium complex stoichiometries and stability constants: , log β(AlLH₋₂) = −6.34 ± 0.02, and log β(AlL₂H₋₁) = −1.14 ± 0.04. The ¹H NMR spectra yielded structural information on species . The ESI-MS data confirmed the metal-ligand stoichiometry of the complexes.The metal-ligand speciation at micromolar Al(III) concentrations (i.e., under in vivo conditions) at physiological pH values reveals that considerable amount of Al(III) is complexed. This suggests that the toxic effect of Al(III) towards cellular membranes might be due to its coordination by protein-bound sialic acid.     

Kinetics and mechanism of the aquation of the trinuclear cation, [μ3-oxo-triaqua-hexakis(acetato)tris(iron(III))]in perchloric acid media

The aquation of the title complex cation in aqueous perchloric acid proceeded via two steps, both postulated to be the proton attack on the oxygen atom which binds the acetate ligand to the metal centre, followed by Fe-O bond cleavage. This was followed by rapid decomposition to produce aqueous iron(III) and acetate ions. The first-order rate constants for the first and second steps at 25 °C are: k₁ = (4.16 ± 0.58) × 10⁻² s⁻¹ and k₂ = (2.09 ± 0.42) × 10⁻³ s⁻¹, respectively, and their corresponding activation parameters are . The spontaneous hydrolysis rate constants for the first and second steps were also determined at 25 °C and ionic strength of 1 mol dm⁻³ and they are k₀ = (3.10 ± 0.82) × 10⁻³ s⁻¹ and , respectively. The corresponding activation parameters are .     

Interaction of gold(I) with thiosulfate-sulfite mixed ligand systems

The system was studied at 25 °C and at I = 0.1 M NaClO₄ using hydrodynamic voltammetry, gold potentiometry, UV-Vis spectrophotometry and Raman spectroscopy. The presence of two mixed-ligand species, Au(S₂O₃)(SO₃)³⁻ and , was detected from the Raman experiments and supported by the gold potentiometric experiments. The stepwise formation constant, log K_11r, for the reaction was found to be 1.1 (r = 1) and 4.8 (r = 2) from the hydrodynamic voltammetric experiments.     

Synthesis and characterization of CpMCl(PR3)(S or W-η-butadienesulfonyl) compounds of rhodium and iridium

A metathesis reaction of [Cp^∗MCl₂(PR₃)] [M = Rh, R = Ph (1), Me (3); M = Ir, R = Ph (2), Me (4)] takes place in the presence of potassium butadienesulfinate (SO₂CHCHCHCH₂)K (9) to afford the mononuclear compounds [Cp^∗M(Cl)(PR₃)(η¹-SO₂CHCHCHCH₂)] [M = Rh, R = Ph (11S), (11W); M = Rh, R = Me (13S), (13W)] and [M = Ir, R = Ph (12S); M = Ir, R = Me (14S), (14W)] under different reaction conditions. The addition of PR₃ (R = Ph, Me) to Cp^∗Ir(Cl)[(1,2,5-η)-SO₂CHCHCHCH₂] (7) affords the corresponding iridium isomers 12S, 12W and 14S, in a non-selective reaction, along with the corresponding dichloride compounds 2 or 4. The ¹H and ¹³C{¹H} NMR data are consistent with the butadienesulfonyl ligands coordinated exclusively through the sulfur atom, and they show the presence of two isomers, described as the S and W conformers, which can be isolated separately. There is clear evidence that these isomers correspond to the kinetic and thermodynamic derivatives, respectively.     

Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding

Specification of the three dimensional structure of a protein from its amino acid sequence, also called a “Grand Challenge” problem, has eluded a solution for over six decades. A modestly successful strategy has evolved over the last couple of decades based on development of scoring functions (e.g. mimicking free energy) that can capture native or native-like structures from an ensemble of decoys generated as plausible candidates for the native structure. A scoring function must be fast enough in discriminating the native from unfolded/misfolded structures, and requires validation on a large data set(s) to generate sufficient confidence in the score. Here we develop a scoring function called pcSM that detects true native structure in the top 5 with 93% accuracy from an ensemble of candidate structures. If we eliminate the native from ensemble of decoys then pcSM is able to capture near native structure (RMSD < = 5 ?) in top 10 with 86% accuracy. The parameters considered in pcSM are a C-alpha Euclidean metric, secondary structural propensity, surface areas and an intramolecular energy function. pcSM has been tested on 415 systems consisting 142,698 decoys (public and CASP—largest reported hitherto in literature). The average rank for the native is 2.38, a significant improvement over that existing in literature. In-silico protein structure prediction requires robust scoring technique(s). Therefore, pcSM is easily amenable to integration into a successful protein structure prediction strategy. The tool is freely available at http://www.scfbio-iitd.res.in/software/pcsm.jsp.     

Modification of aminoallenylidene complexes of chromium via exchange of the C3-bound amino group

The aminoallenylidene(pentacarbonyl)chromium complexes [(CO)₅CrCCC(NR¹R²)Ph] (1a-c) react with dimethylamine by addition of the amine to the C1C2 bond of the allenylidene ligand to give alkenyl(amino)carbene complexes [(CO)₅CrC(NMe₂)CHC(NR¹R²)Ph] (2a-c) (R¹ = Me: R² = Me (a), Ph (b); R¹ = Et: R² = Ph (c)). In contrast, addition of a large excess (usually 20 equivalents) of ammonia or primary amines, H₂NR, to solutions of [(CO)₅CrCCC(NMe₂)Ph] (1a) affords the aminoallenylidene complexes [(CO)₅CrCCC(NHR)Ph] (1d-w) in which the dimethylamino group is replaced by NH₂ or NHR, respectively. In addition to simple amines such as methylamine, butylamine, and aniline, amines carrying a functional group (allylamine, propargylamine) and amino acid esters as well as amino terpenes and amino sugars can be used to displace the NMe₂ substituent. Usually the Z isomer (with respect to the partial C3-N double bond) is formed exclusively. Products derived from addition of H₂NR to the C1C2 bond of 1a are not observed. The amino group in 1d-w is rapidly deprotonated by excess of amine to form iminium alkynyl chromates [1d-w]⁻, thus protecting 1d-w from addition of free amine to either C3 or across the C1C2 bond. The iminium alkynyl chromates are readily reprotonated by acids or by chromatography on wet SiO₂ to reform 1d-w.     

The contribution of SNAT1 to system A amino acid transporter activity in human placental trophoblast

System A-mediated amino acid transport across the placenta is important for the supply of neutral amino acids needed for fetal growth. All three system A subtypes (SNAT1, 2, and 4) are expressed in human placental trophoblast suggesting there is an important biological role for each. Placental system A activity increases as pregnancy progresses, coinciding with increased fetal nutrient demands. We have previously shown SNAT4-mediated system A activity is higher in first trimester than at term, suggesting that SNAT1 and/or SNAT2 are responsible for the increased system A activity later in gestation. However, the relative contribution of each subtype to transporter activity in trophoblast at term has yet to be evaluated. The purpose of this study was to identify the predominant subtype of system A in cytotrophoblast cells isolated from term placenta, maintained in culture for 66 h, by: (1) measuring mRNA expression of the three subtypes and determining the Michaelis-Menten constants for uptake of the system A-specific substrate, ¹⁴C-MeAIB, (2) investigating the contribution of SNAT1 to total system A activity using siRNA. Results: mRNA expression was highest for the SNAT1 subtype of system A. Kinetic analysis of ¹⁴C-MeAIB uptake revealed two distinct transport systems; system 1: K_m = 0.38 ± 0.12 mM, V_max = 27.8 ± 9.0 pmol/mg protein/20 min, which resembles that reported for SNAT1 and SNAT2 in other cell types, and system 2: K_m = 45.4 ± 25.0 mM, V_max = 1190 ± 291 pmol/mg protein/20 min, which potentially represents SNAT4. Successful knockdown of SNAT1 mRNA using target-specific siRNA significantly reduced system A activity (median 75% knockdown, n = 7). Conclusion: These data enhance our limited understanding of the relative importance of the system A subtypes for amino acid transport in human placental trophoblast by demonstrating that SNAT1 is a key contributor to system A activity at term.     

Synthesis and reactivity of iron carbonyl clusters containing alkynethiolate ligands

The new cluster Li[Fe₃(μ₃,η¹-SCCFc)(CO)₉] reacts with ClAuPPh₃ to afford compound [Fe₃Au(μ₄,η²-CCFc)(CO)₉(PPh₃)], which exhibits an isomeric equilibrium in solution with the cluster [Fe₃Au(μ₃,η²-CCFc)(CO)₉(PPh₃)].The rupture of C-S bonds in the thioethers Me₃SiCCSCCR (R = Fc, SiⁱPr₃) in the presence of Fe₃(CO)₁₂, yields to the clusters [Fe₃(μ-SCCSiⁱPr₃)(μ-CCSiMe₃)(CO)₉] and [Fe₃(μ,η²-(SiⁱPr₃)CCCCSiMe₃)(μ₃-S)(CO)₉] together with the unexpected compounds [Fe₂(μ-SCC(H)R)(CO)₆] (R = SiMe₃, SiⁱPr₃).Additionally, the dinuclear derivatives [Fe₂(μ-SCCR)(μ-CCR′)(CO)₆] (R = Fc, R′ = SiMe₃; R = SiMe₃, R′ = Fc; R = SiMe₃; R′ = SiⁱPr₃) have also been obtained. These compounds have been spectroscopically characterized and the crystal structure of some of them has been solved.     

The first examples of benzidinium cations templated low-dimensional molybdates

For the first time, use of benzidine as a structure-directing agent has resulted in the crystallization of two novel organic/inorganic hybrid molybdates under hydrothermal condition (180 °C and autogenous pressure). The presence of monoprotonated benzidinium ions in aqueous molybdate solution appears to engineer two new hybrid solids: one-dimensional chains in [H₂NC₁₂H₈NH₃]₂Mo₂O₇, 1 (a = 5.9686, b = 7.0761 and c = 14.3293 Å, α = 77.17°, β = 85.25° and γ = 88.56°; and Z = 2) and two-dimensional step-wise layered molybdate [H₂NC₁₂H₈NH₃]₂Mo₅O₁₆, 2 (a = 5.6843, b = 14.3024 and c = 19.4787Å, α = 108.1°, β = 98.4° and γ = 90.0°; , Z = 2). 1 is an unusual solid wherein the anionic chains are charge compensated by counter cations which also act as ligands to the metal and 2 is a new layered molybdate built of MoO₅ square pyramids and MoO₆ octahedra.     

Reaction of Mo(CO)4(NCCH3)2 and 7-aza-2-Tosylnorbornadiene

Reaction of Mo(CO)₄(NCCH₃)₂ and 7-aza-2-tosylnorbornadiene (7-azaNBD) yielded five air-stable Mo complexes. One is Mo(CO)₄(η⁴-7-azaNBD), in which the molybdenum atom is chelated by the two π-bonds of 7-azaNBD. The other four are isomers of Mo(CO)₂(η²-7-azaNBD)₂, in which the molybdenum atoms are chelated by the nitrogen atom and one of the two double bonds of 7-azaNBD. In one pair of the isomers, the metal binds to C(2)C(3) of both 7-azaNBD ligands; whereas in the other pair of isomers the metal binds to C(2)C(3) of one 7-azaNBD ligand and C(5)C(6) of another ligand. All structures were fully characterized by NMR spectra. A single crystal of compound 4 was analyzed by X-ray diffraction analysis, which was found to be monoclinic with a = 8.4199, b = 23.984, c = 16.395 Å, and β = 99.99°.     

Ferrocene- and ruthenocene-containing chalcones: A spectroscopic and electrochemical study

Chalcones of the type Mc-CO-CHCH-Ph, Ph-CO-CHCH-Mc and Mc-CO-CHCH-Mc with Mc = Fc = ferrocenyl or Rc = ruthenocenyl, and Ph = phenyl were synthesized. Synthesis was achieved by base catalyzed Claisen-Schmidt condensation of the appropriated acetyl and aldehyde in ethanol. Cyclic voltammetry in CH₃CN in the presence of 0.1 mol dm⁻³ [N(Bu)₄][PF₆] revealed chemical and electrochemical reversible behaviour for the Fc/Fc⁺ couple and irreversible electrochemistry for the two electron Rc/Rc²⁺ couple. The potential ranges for the Fc/Fc⁺ couple varied in the range 138 ? E°′ ? 302 mV while E_pa for Rc/Rc²⁺ couple was between 358 and 510 mV vs. FcH/FcH⁺, the internal standard. Chalcones with the carbonyl group adjacent to the metallocene, are more difficult to oxidize.     

Presep: Predicting the Propensity of a Protein Being Secreted into the Supernatant when Expressed in Pichia pastoris

Pichia pastoris is commonly used for the production of recombinant proteins due to its preferential secretion of recombinant proteins, resulting in lower production costs and increased yields of target proteins. However, not all recombinant proteins can be successfully secreted in P. pastoris. A computational method that predicts the likelihood of a protein being secreted into the supernatant would be of considerable value; however, to the best of our knowledge, no such tool has yet been developed. We present a machine-learning approach called Presep to assess the likelihood of a recombinant protein being secreted by P. pastoris based on its pseudo amino acid composition (PseAA). Using a 20-fold cross validation, Presep demonstrated a high degree of accuracy, with Matthews correlation coefficient (MCC) and overall accuracy (Q2) scores of 0.78 and 95%, respectively. Computational results were validated experimentally, with six β-galactosidase genes expressed in P. pastoris strain GS115 to verify Presep model predictions. A strong correlation (R² = 0.967) was observed between Presep prediction secretion propensity and the experimental secretion percentage. Together, these results demonstrate the ability of the Presep model for predicting the secretion propensity of P. pastoris for a given protein. This model may serve as a valuable tool for determining the utility of P. pastoris as a host organism prior to initiating biological experiments. The Presep prediction tool can be freely downloaded at http://www.mobioinfor.cn/Presep.     

Silver(I) acetylides stabilized by η-alkynes: Synthesis, reaction chemistry and solid state structures

Individual synthetic routes to heterobimetallic Ti(IV)-Ag(I) acetylides of type {[Ti](μ-σ,π-CCR¹)₂}AgCCR² ([Ti] = (η⁵-C₅H₄SiMe₃)₂Ti: R¹ = SiMe₃: 6, R² = SiMe₃; 7, R² = Ph. R¹ = ^tBu: 8, R² = SiMe₃; 9, R² = Ph. [Ti] = (η⁵-C₅H₅)₂Ti): 10, R¹ = ^tBu, R² = SiMe₃) including (i) the reaction of {[Ti](μ-σ, π-CCR¹)₂}AgNO₃ ([Ti] = (η⁵-C₅H₄SiMe₃)₂Ti): 1, R¹ = SiMe₃; 2, R¹ = ^tBu. [Ti] = (η⁵-C₅H₅)₂Ti: 3, R¹ = ^tBu) with LiCCR² (4, R² = SiMe₃; 5, R² = Ph) and (ii) treatment of [Ti](CCSiMe₃)₂ ([Ti] = (η⁵-C₅H₄SiMe₃)₂Ti) (11) with [AgCCR²] (12, R² = SiMe₃; 13, R² = Ph) are described. The reactions of 1-3 with 4 or 5 appeared to be sensitive towards stoichiometry because an excess of 4 or 5 resulted in the formation of [(Ag(CCR²)₂)Li(OEt₂)]_n (14) and [Ti](CCR¹)₂. Coordination polymer 14 is also accessible, when, for example, [AgCCSiMe₃] (12) is treated with 1 eq. of LiCCSiMe₃ (4) in diethyl ether.The titanium(IV)-silver(I) acetylides 6-10 are stable in the dark and at low temperature, while on exposure to light and on heating they decompose to give R²CC-CCR² together with [Ti](CCR¹)₂ and elemental silver.Complexes 6-10 contain a mono-nuclear AgCCR² entity stabilized by the chelate-bonded organometallic π-tweezer molecule [Ti](CCSiMe₃)₂, which was evinced by structure determination of 7 in the solid state. In 14 linear [Me₃SiCC-Ag-CCSiMe₃]⁻ units are connected by [Li(OEt₂)]⁺ building blocks forming a coordination polymer.