XANES study of iron displacement in the haem of myoglobin

The XANES (X‐ray absorption near edge structure) spectra of deoxy human adult haemoglobin (HbA) and myoglobin (Mb) have been measured at the wiggler beam line of the Frascati synchrotron radiation facility. The XANES are interpreted by the multiple scattering cluster theory. The variations in the XANES between HbA and Mb are assigned to changes in the Fe‐porphyrin geometry

Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\alpha}1{\beta}2 and {\alpha}2{\beta}1 interface.Comment: Reprinted (adapted) with permission from J. Phys. Chem. B DOI:10.1021/jp3022908. Copyright (2012) American Chemical Societ

Benchmarking of Halogen Bond Strength in Solution with Nickel Fluorides : Bromine versus Iodine and Perfluoroaryl versus Perfluoroalkyl Donors

The energetics of halogen bond formation in solution have been investigated for a series of nickel fluoride halogen bond acceptors; trans-[NiF(2-C 5NF 4)(PEt 3) 2] (A1), trans-[NiF{2-C 5NF 3(4-H)}(PEt 3) 2] (A2), trans-[NiF{2-C 5NF 3(4-NMe 2)}(PEt 3) 2] (A3) and trans-[NiF{2-C 5NF 2H(4-CF 3)}(PCy 3) 2] (A4) with neutral organic halogen bond donors, iodopentafluorobenzene (D1), 1-iodononafluorobutane (D2) and bromopentafluorobenzene (D3), in order to establish the significance of changes from perfluoroaryl to perfluoroalkyl donors and from iodine to bromine donors. 19F NMR titration experiments have been employed to obtain the association constants, enthalpy, and entropy for the halogen bond formed between these donor-acceptor partners in protiotoluene. For A2–A4, association constants of the halogen bonds formed with iodoperfluoroalkane (D2) are consistently larger than those obtained for analogous complexes with the iodoperfluoroarene (D1). For complexes formed with A2–A4, the strength of the halogen bond is significantly lowered upon modification of the halogen donor atom from I (in D1) to Br (in D3) (for D1: 5≤K 285≤12 m −1, for D3: 1.0≤K 193≤1.6 m −1). The presence of the electron donating NMe 2 substituent on the pyridyl ring of acceptor A3 led to an increase in −ΔH, and the association constants of the halogen bond complexes formed with D1–D3, compared to those formed by A1, A2 and A4 with the same donors

Computational studies explain the importance of two different substituents on the chelating bis(amido) ligand for transfer hydrogenation by bifunctional Cp*Rh(III) catalysts

A computational approach (DFT-B3PW91) is used to address previous experimental studies (Chem. Commun. 2009, 6801) that showed that transfer hydrogenation of a cyclic imine by Et3N·HCO2H in dichloromethane catalyzed by 16-electron bifunctional Cp*Rh III(XNC6H4NX') is faster when XNC 6H4NX' = TsNC6H4NH than when XNC6H4NX' = HNC6H4NH or TsNC 6H4NTs (Cp* = η5-C5Me 5, Ts = toluenesulfonyl). The computational study also considers the role of the formate complex observed experimentally at low temperature. Using a model of the experimental complex in which Cp* is replaced by Cp and Ts by benzenesulfonyl (Bs), the calculations for the systems in gas phase reveal that dehydrogenation of formic acid generates CpRhIIIH(XNC 6H4NX'H) via an outer-sphere mechanism. The 16-electron Rh complex + formic acid are shown to be at equilibrium with the formate complex, but the latter lies outside the pathway for dehydrogenation. The calculations reproduce the experimental observation that the transfer hydrogenation reaction is fastest for the nonsymmetrically substituted complex CpRh III(XNC6H4NX') (X = Bs and X' = H). The effect of the linker between the two N atoms on the pathway is also considered. The Gibbs energy barrier for dehydrogenation of formic acid is calculated to be much lower for CpRhIII(XNCHPhCHPhNX') than for CpRh III(XNC6H4NX') for all combinations of X and X'. The energy barrier for hydrogenation of the imine by the rhodium hydride complex is much higher than the barrier for hydride transfer to the corresponding iminium ion, in agreement with mechanisms proposed for related systems on the basis of experimental data. Interpretation of the results by MO and NBO analyses shows that the most reactive catalyst for dehydrogenation of formic acid contains a localized Rh-NH π-bond that is associated with the shortest Rh-N distance in the corresponding 16-electron complex. The asymmetric complex CpRhIII(BsNC6H4NH) is shown to generate a good bifunctional catalyst for transfer hydrogenation because it combines an electrophilic metal center and a nucleophilic NH group

Light-Induced Activation of a Molybdenum Oxotransferase Model within a Ru(II)-Mo(VI) Dyad

Nature uses molybdenum-containing enzymes to catalyze oxygen atom transfer (OAT) from water to organic substrates. In these enzymes, the two electrons that are released during the reaction are rapidly removed, one at a time, by spatially separated electron transfer units. Inspired by this design, a Ru(II)-Mo(VI) dyad was synthesized and characterized, with the aim of accelerating the rate-determining step in the cis-dioxo molybdenum-catalyzed OAT cycle, the transfer of an oxo ligand to triphenyl phosphine, via a photo-oxidation process. The dyad consists of a photoactive bis(bipyridyl)-phenanthroline ruthenium moiety that is covalently linked to a bioinspired cis-dioxo molybdenum thiosemicarbazone complex. The quantum yield and luminescence lifetimes of the dyad [Ru(bpy)2(L(2))MoO2(solv)](2+) were determined. The major component of the luminescence decay in MeCN solution (τ = 1149 ± 2 ns, 67%) corresponds closely to the lifetime of excited [Ru(bpy)2(phen-NH2)](2+), while the minor component (τ = 320 ± 1 ns, 31%) matches that of [Ru(bpy)2(H2-L(2))](2+). In addition, the (spectro)electrochemical properties of the system were investigated. Catalytic tests showed that the dyad-catalyzed OAT from dimethyl sulfoxide to triphenyl phosphine proceeds significantly faster upon irradiation with visible light than in the dark. Methylviologen acts as a mediator in the photoredox cycle, but it is regenerated and hence only required in stoichiometric amounts with respect to the catalyst rather than sacrificial amounts. It is proposed that oxidative quenching of the photoexcited Ru unit, followed by intramolecular electron transfer, leads to the production of a reactive one-electron oxidized catalyst, which is not accessible by electrochemical methods. A significant, but less pronounced, rate enhancement was observed when an analogous bimolecular system was tested, indicating that intramolecular electron transfer between the photosensitizer and the catalytic center is more efficient than intermolecular electron transfer between the separate components

Platinum(0)-mediated C–O bond activation of ethers via an SN2 mechanism

A computational study of the C(methyl)–O bond activation of fluorinated aryl methyl ethers by a platinum(0) complex Pt(PCyp3)2 (Cyp = cyclopentyl) (N. A. Jasim, R. N. Perutz, B. Procacci and A. C. Whitwood, Chem. Commun., 2014, 50, 3914) demonstrates that the reaction proceeds via an SN2 mechanism. Nucleophilic attack of Pt(0) generates an ion pair consisting of a T-shaped platinum cation with an agostic interaction with a cyclopentyl group and a fluoroaryloxy anion. This ion-pair is converted to a 4-coordinate Pt(II) product trans-[PtMe(OArF)(PCyp3)2]. Structure-reactivity correlations are fully consistent with this mechanism. The Gibbs energy of activation is calculated to be substantially higher for aryl methyl ethers without fluorine substituents and higher still for alkyl methyl ethers. These conclusions are in accord with the experimental results. Further support was obtained in an experimental study of the reaction of Pt(PCy3)2 with 2,3,5,6-tetrafluoro-4-allyloxypyridine yielding the salt of the Pt(η3-allyl) cation and the tetrafluoropyridinolate anion [Pt(PCy3)2(η3-allyl)][OC5NF4]. The calculated activation energy for this reaction is significantly lower than that for fluorinated aryl methyl ethers

Local Simulation Algorithms for Coulomb Interaction

Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow equilibration using a local Hamiltonian. The method introduces an auxiliary field with constrained dynamics so that the equilibrium distribution is determined by the Coulomb interaction. We demonstrate the efficiency of the method by simulating a simple, charged lattice gas.Comment: Last figure changed to improve demonstration of numerical efficienc

Laser-Induced Fluorescence of Molybdenocene and Tungstenocene in Low-Temperature Matrices

The reactive metallocenes, tungstenocene and molybdenocene (M(t75-C5H5)2; M = Mo, W), have been generated by photolysis of the corresponding dihydride complexes, M(í;5-C5H5)2H2, in argon and nitrogen matrices at 12 K. The metallocenes have been probed by laser-induced fluorescence with a pulsed tunable laser and by UV/vis absorption spectroscopy. Structured emission is observed from the LMCT excited states (lifetimes < 10 ns). The spectra are complicated by multiple sites/conformers, but emission spectra of a single site/ conformer may be obtained with appropriate selection of matrix and excitation wavelength. Corresponding excitation spectra are measured from the area of selected emission peaks as a function of excitation wavelength. Vibrational progressions are dominated by the ring—metal-ring symmetric stretching mode (v4 ~ 300 cm-1). Nevertheless, this mode changes in frequency by <4 cm-1 (< 1.3%) in the LMCT excited state. The bestresolved peaks have a full width at half-maximum of ca. 10 cm-1. Most of the emission is vibrationally fully relaxed, but weak emission peaks arising from ' = 1 states are found for MoCp2 in N2 matrices

Kinetics of stochastically-gated diffusion-limited reactions and geometry of random walk trajectories

In this paper we study the kinetics of diffusion-limited, pseudo-first-order A + B -> B reactions in situations in which the particles' intrinsic reactivities vary randomly in time. That is, we suppose that the particles are bearing "gates" which interchange randomly and independently of each other between two states - an active state, when the reaction may take place, and a blocked state, when the reaction is completly inhibited. We consider four different models, such that the A particle can be either mobile or immobile, gated or ungated, as well as ungated or gated B particles can be fixed at random positions or move randomly. All models are formulated on a $d$-dimensional regular lattice and we suppose that the mobile species perform independent, homogeneous, discrete-time lattice random walks. The model involving a single, immobile, ungated target A and a concentration of mobile, gated B particles is solved exactly. For the remaining three models we determine exactly, in form of rigorous lower and upper bounds, the large-N asymptotical behavior of the A particle survival probability. We also realize that for all four models studied here such a probalibity can be interpreted as the moment generating function of some functionals of random walk trajectories, such as, e.g., the number of self-intersections, the number of sites visited exactly a given number of times, "residence time" on a random array of lattice sites and etc. Our results thus apply to the asymptotical behavior of the corresponding generating functions which has not been known as yet.Comment: Latex, 45 pages, 5 ps-figures, submitted to PR

The Contrasting Character of Early and Late Transition Metal Fluorides as Hydrogen Bond Acceptors

The association constants and enthalpies for the binding of hydrogen bond donors to group 10 transition metal complexes featuring a single fluoride ligand (trans-[Ni(F)(2-C5NF4)(PR3)2], R = Et 1a, Cy 1b, trans-[Pd(F)(4-C5NF4)(PCy3)2] 2, trans-[Pt(F){2-C5NF2H(CF3)}(PCy3)2] 3 and of group 4 difluorides (Cp2MF2, M = Ti 4a, Zr 5a, Hf 6a; Cp2MF2, M = Ti 4b, Zr 5b, Hf 6b) are reported. These measurements allow placement of these fluoride ligands on the scales of organic H-bond acceptor strength. The H-bond acceptor capability β (Hunter scale) for the group 10 metal fluorides is far greater (1a 12.1, 1b 9.7, 2 11.6, 3 11.0) than that for group 4 metal fluorides (4a 5.8, 5a 4.7, 6a 4.7, 4b 6.9, 5b 5.6, 6b 5.4), demonstrating that the group 10 fluorides are comparable to the strongest organic H-bond acceptors, such as Me3NO, whereas group 4 fluorides fall in the same range as N-bases aniline through pyridine. Additionally, the measurement of the binding enthalpy of 4-fluorophenol to 1a in carbon tetrachloride (?23.5 ± 0.3 kJ mol-1) interlocks our study with Laurence's scale of H-bond basicity of organic molecules. The much greater polarity of group 10 metal fluorides than that of the group 4 metal fluorides is consistent with the importance of p?-d? bonding in the latter. The polarity of the group 10 metal fluorides indicates their potential as building blocks for hydrogen-bonded assemblies. The synthesis of trans-[Ni(F){2-C5NF3(NH2)}(PEt3)2], which exhibits an extended chain structure assembled by hydrogen bonds between the amine and metal-fluoride groups, confirms this hypothesis