Binding sites of nitrogenase: kinetic and theoretical studies of cyanide binding to extracted FeMo-cofactor derivatives

The first kinetic study of a substrate (CN(-)) binding to the isolated active site (extracted FeMo-cofactor) of nitrogenase is described. The kinetics of the reactions between CN(-) and various derivatives of extracted FeMo-cofactor [FeMoco-L; where L is bound to Mo, and is NMF, Bu(t)NC, or imidazole (ImH)] have been followed using a stopped-flow, sequential-mix method in which the course of the reaction is followed indirectly, by monitoring the change in the rate of the reaction of the cofactor with PhS(-). The kinetic results, together with DFT calculations, indicate that the initial site of CN(-) binding to FeMoco-L is controlled by a combination of the electron-richness of the cluster core and lability of the Mo-L bond. Ultimately, the reactions between FeMoco-L and CN(-) involve displacement of L and binding of CN(-) to Mo. These reactions occur with a variety of rates and rate laws dependent on the nature of L. For FeMoco-NMF, the reaction with CN(-) is complete within the dead-time of the apparatus (ca. 4 ms), while with FeMoco-CNBu(t) the reaction is much slower and exhibits first order dependences on the concentrations of both FeMoco-CNBu(t) and CN(-) (k = 2.5 +/- 0.5 x 10(4) dm(3) mol(-1) s(-1)). The reaction of FeMoco-ImH with CN(-) occurs at a rate which exhibits a first order dependence on FeMoco-ImH but is independent of the concentration of CN(-) (k = 50 +/- 10 s(-1)). The results are interpreted in terms of CN(-) binding directly to the Mo site for FeMoco-NMF and FeMoco-ImH, but with FeMoco-CNBu(t) initial binding at an Fe site is followed by movement of CN(-) to Mo. Complementary DFT calculations are consistent with this interpretation, indicating that, in FeMoco-L, the Mo-L bond is stronger for L = ImH than for L = CNBu(t) and the binding of CN(-) to Mo is stronger than to any Fe atom in the cofactor.     

Tailoring the cavities of hydrogen-bonded amphidynamic crystals using weak contacts: towards faster molecular machines

This work describes the use of C–H⋯F–C contacts in the solid-state from the stator towards the rotator to fine-tune their internal motion, by constructing a set of interactions that generate close-fitting cavities in three supramolecular rotors 1–3I. The crystal structures of these rotors, determined by synchrotron radiation experiments at different temperatures, show the presence of such C–H⋯F–C contacts between extended carbazole stators featuring fluorinated phenyl rings and the 1,4-diazabicyclo[2.2.2]octane (DABCO) rotator. According to the ²H NMR results, using deuterated samples, and periodic density functional theory computations, the rotators experience fast angular displacements (preferentially 120° jumps) due to their low rotational activation energies (E_a = 0.8–2.0 kcal mol⁻¹). The higher rotational barrier for 1 (2.0 kcal mol⁻¹) is associated with a larger number of weak C–H⋯F–C contacts generated by the stators. This strategy offers the possibility to explore the correlation among weak intermolecular forces, cavity shape, and internal dynamics, which has strong implications in the design of future fine-tuned amphidynamic crystals.

This work describes the use of C–H⋯F–C contacts in the solid-state from the stator towards the rotator to fine-tune their internal motion, by constructing a set of interactions that generate close-fitting cavities in three supramolecular rotors 1–3I.     

Correlating axial and equatorial ligand field effects to the single-molecule magnet performances of a family of dysprosium bis-methanediide complexes

Treatment of the new methanediide–methanide complex [Dy(SCS)(SCSH)(THF)] (1Dy, SCS = {C(PPh₂S)₂}²⁻) with alkali metal alkyls and auxillary ethers produces the bis-methanediide complexes [Dy(SCS)₂][Dy(SCS)₂(K(DME)₂)₂] (2Dy), [Dy(SCS)₂][Na(DME)₃] (3Dy) and [Dy(SCS)₂][K(2,2,2-cryptand)] (4Dy). For further comparisons, the bis-methanediide complex [Dy(NCN)₂][K(DB18C6)(THF)(toluene)] (5Dy, NCN = {C(PPh₂NSiMe₃)₂}²⁻, DB18C6 = dibenzo-18-crown-6 ether) was prepared. Magnetic susceptibility experiments reveal slow relaxation of the magnetisation for 2Dy–5Dy, with open magnetic hysteresis up to 14, 12, 15, and 12 K, respectively (∼14 Oe s⁻¹). Fitting the alternating current magnetic susceptibility data for 2Dy–5Dy gives energy barriers to magnetic relaxation (U_eff) of 1069(129)/1160(21), 1015(32), 1109(70), and 757(39) K, respectively, thus 2Dy–4Dy join a privileged group of SMMs with U_eff values of ∼1000 K and greater with magnetic hysteresis at temperatures >10 K. These structurally similar Dy-components permit systematic correlation of the effects of axial and equatorial ligand fields on single-molecule magnet performance. For 2Dy–4Dy, the Dy-components can be grouped into 2Dy–cation/4Dy and 2Dy–anion/3Dy, where the former have almost linear C Dy C units with short average Dy C distances, and the latter have more bent C Dy C units with longer average Dy C bonds. Both U_eff and hysteresis temperature are superior for the former pair compared to the latter pair as predicted, supporting the hypothesis that a more linear axial ligand field with shorter M–L distances produces enhanced SMM properties. Comparison with 5Dy demonstrates unusually clear-cut examples of: (i) weakening the equatorial ligand field results in enhancement of the SMM performance of a monometallic system; (ii) a positive correlation between U_eff barrier and axial linearity in structurally comparable systems.

Studies on equatorial donor and C Dy C angle variation effects on energy barriers to the slow relaxation of magnetisation are reported.     

Synthesis, crystal structure, and chirality of divalent lanthanide reagents containing tri- and tetraglyme

Six new divalent lanthanide complexes using triglyme (trigly) and tetraglyme (tetgly) as achiral ligands have been prepared, using a facile synthetic method, in search for enantioselective solid-state reagents. The crystal structures of cis-[SmI₂(trigly)thf] (1), trans-[YbI₂(trigly)thf] (2), trans-[SmI₂(trigly)dme] (3), trans-[YbI₂(tetgly)] (4), trans-[EuI₂(tetgly)thf] (5), and [Sm(tetgly)₂][SmI₃(tetgly)]I (6) have been determined. All complexes, except 5, are chiral. The 10-coordinate cation in 6 displays a helical chirality since the two tetraglyme ligands are wrapped around the samarium ion. Since trans-[YbI₂(tetgly)] (4), which has a chiral arrangement of terminal methyl groups, crystallizes as a conglomerate, preferential crystallization and consequent enantioselective reduction of acetophenone was attempted, but resulted in racemic products, possibly on account of racemic twinning in 4.     

Bis(Cyclodisilazan-1-yl)dimethylsilane Synthese und Reaktionen

Bis(cyclodisilazane-1-yl) dimethylsilanes — Synthesis and Reactions The monolithium derivate of trisilazan-1-yl-cyclodisilazane 1 reacts with F₃SiN (SiMe₃)₂ with substitution. The silyl-bridged cyclodisilazanes 3–6 are formed in the reaction of the dilithium derivate of 1 with fluoro- and chlorosilanes. Using lithiumamide and lithiummethanolate a controlled exchange of one fluoro atom of 4 occurs ( 7,8 ). 9 and 10 are formed by hydrolysis of 4 . The aminofunctional compounds 11 und 12 are obtained in the reaction of 5 and 6 with NH₃. The dispirocyclus 13 is formed in the reaction of 8 with tert.-butyllithium. The reaction of dilithiated 1 with 4 gives the spirocyclus 14 . The crystal structure of 14 is discussed.     

Theory of semiclassical transition probabilities for inelastic and reactive collisions. IV. Classically-inaccessible transitions calculated by integration along complex-valued trajectories

We calculate semiclassical S-matrix elements S_mn by numerical integration along complex-valued trajectories, by avoiding (simply) previously reported trajectory divergences. Now, one can numerically calculate even ? S_mn? ≈ 10⁻¹¹ for the Secrest-Johnson system (their lowest ? S_mn?²), instead of only ? S_mn?² > 10⁻³. Agreement is excellent.     

Organic synthesis on the microgram scale. III separation and purification of steroids

Summary This paper describes techniques for separation and purification of steroids on the thin-layer plate. Two or more operations can be performed on the same plate in order to avoid loss of material and product.When a steroid diketone (progesterone) is treated with 2,4-dinitrophenylhydrazine on silica gel, three products are obtainable. These compounds can be readily purified on the same thin-layer plate and converted to the parent steroid by means of stannous chloride in dilute hydrochloric acid.

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Zusammenfassung Trennung und Reinigung von Steroiden auf der Dünnschichtplatte werden beschrieben. Zwei oder mehr Operationen lassen sich, um Substanzverluste zu vermeiden, auf derselben Platte ausführen.Wird ein Diketosteroid (Progesteron) mit 2,4-Dinitrophenylhydrazin auf Kieselgel behandelt, so erhält man drei Reaktionsprodukte, die auf derselben Platte leicht gereinigt und mit Zinn(II)-chlorid in verd. Salzsäure in das entsprechende Ausgangssteroid zurückverwandelt werden können.

     

Modern microscopy methods for the structural study of porous materials

This article describes a number of important recent microscopy tools and their application in particular to the study of porous inorganic materials. The authors believe that these new techniques are on the threshold of delivering enormous new power in the chemist's arsenal for understanding new and complex behaviour in multi-component, hierarchical or composite materials. In particular we consider the contribution of electron crystallography, three-dimensional electron tomography, ultra-high resolution scanning electron microscopy as well as the combined application of high-resolution electron microscopy and atomic force microscopy to the study of surfaces and crystal growth. Much of this work has taken on a particular significance owing to the ground breaking work of scientists at Mobil and in Japan 10 years ago in the successful synthesis of materials with porosity on many length scales achieved through the cooperative self-assembly between inorganic and organic phases. This resulted in a series of materials known as M41S of which MCM-41 and MCM-48 were two of the first and most important structures to be synthesised. This has led to a wealth of new porous structures with order over many length scales and has presented new problems in characterisation. Microscopy methods properly executed are particularly important in the study of this new class of material.     

Development of a formulation of Pirodavir using 2-hydroxypropyl-β-cyclodextrin

Pirodavir, 4-[2-[1-(6-Methyl-3-pyridazinyl)-4-piperidinyl]ethoxy]benzoic acid ethyl ester, is an antiviral compound which has low aqueous solubility (<0.01 mg/ml). The compound is a weak base (pKa 5.8) with high lipophicity (logP 4.44). Ionization of the compound increases the solubility in acidic medium to 2.3 mg/ml at pH 2.4. However, a low pH is not acceptable for nasal application as this would induce irritation. Extensive solubility studies were performed using different types of substituted cyclodextrins in order to select an appropriate derivate capable of increasing solubility to an acceptable level for formulations for nasal application. Aqueous solubility of pirodavir increased in a linear fashion with increasing concentration of most of the substituted cyclodextrins. However, using 2-hydropropyl-β-cyclodextrin (HPBCD) the solubility increased in a non-linear fashion. Based on these studies HPBCD was selected as the most appropriate excipient. To support a clinical study on the treatment of rhinovirus cold by intranasal Pirodavir formulations were developed containing up to 5 mg/ml of pirodavir and up to 10% of HPBCD. Stability of the formulations was studied and found to be acceptable.     

A global investigation of phase equilibria using the perturbed-chain statistical-associating-fluid-theory approach

The recently developed perturbed-chain statistical-associating-fluid theory (PC-SAFT) is investigated for a wide range of model parameters including the parameter m representing the chain length and the thermodynamic temperature T and pressure p. This approach is based upon the first-order thermodynamic perturbation theory for chain molecules developed by Wertheim [M. S. Wertheim, J. Stat. Phys. 35, 19 (1984); ibid. 42, 459 (1986)] and Chapman et al. [G. Jackson, W. G. Chapman, and K. E. Gubbins, Mol. Phys. 65, 1 (1988); W. G. Chapman, G. Jackson, and K. E. Gubbins, ibid. 65, 1057 (1988)] and includes dispersion interactions via the second-order perturbation theory of Barker and Henderson [J. A. Barker and D. Henderson, J. Chem. Phys. 47, 4714 (1967)]. We systematically study a hierarchy of models which are based on the PC-SAFT approach using analytical model calculations and Monte Carlo simulations. For one-component systems we find that the analytical model in contrast with the simulation results exhibits two phase-separation regions in addition to the common gas-liquid coexistence region: One phase separation occurs at high density and low temperature. The second demixing takes place at low density and high temperature where usually the ideal-gas phase is expected in the phase diagram. These phenomena, which are referred to as "liquid-liquid" and "gas-gas" equilibria, give rise to multiple critical points in one-component systems, as well as to critical end points and equilibria of three fluid phases, which can usually be found in multicomponent mixtures only. Furthermore, it is shown that the liquid-liquid demixing in this model is not a consequence of a "softened" repulsive interaction as assumed in the theoretical derivation of the model. Experimental data for the melt density of polybutadiene with molecular mass Mw=45,000 gmol are correlated here using the PC-SAFT equation. It is shown that the discrepancies in modeling the polymer density at ambient temperature and high pressure can be traced back to the liquid-liquid phase separation predicted by the equation of state at low temperatures. This investigation provides a basis for understanding possible inaccuracies or even unexpected phase behavior which can occur in engineering applications of the PC-SAFT model aiming at predicting properties of macromolecular substances.