Alternating carrier models of asymmetric glucose transport violate the energy conservation laws

Alternating access transporters with high-affinity externally facing sites and low-affinity internal sites relate substrate transit directly to the unliganded asymmetric “carrier” (Cⁱ) distribution. When both bathing solutions contain equimolar concentrations of ligand, zero net flow of the substrate-carrier complex requires a higher proportion of unliganded low-affinity inside sites () and slower unliganded “free” carrier transit from inside to outside than in the reverse direction. However, asymmetric rates of unliganded carrier movement, k_ij, imply that an energy source, ΔG_carrier = RT ln (k_oi/k_io) = RT ln (Cⁱⁿ/C^out) = RT ln (), where R is the universal gas constant (8.314 Joules/M/K°), and T is the temperature, assumed here to be 300 K°, sustains the asymmetry. Without this invalid assumption, the constraints of carrier path cyclicity, combined with asymmetric ligand affinities and equimolarity at equilibrium, are irreconcilable, and any passive asymmetric uniporter or cotransporter model system, e.g., Na-glucose cotransporters, espousing this fundamental error is untenable. With glucose transport via GLUT1, the higher maximal rate and K_m of net ligand exit compared to net ligand entry is only properly simulated if ligand transit occurs by serial dissociation-association reactions between external high-affinity and internal low-affinity immobile sites. Faster intersite transit rates occur from lower-affinity sites than from higher-affinity sites and require no other energy source to maintain equilibrium. Similar constraints must apply to cotransport.     

Applicability of new spin trap agent, 2-diphenylphosphinoyl-2-methyl-3,4-dihydro-2H-pyrrole N-oxide, in biological system

Electron spin resonance using spin-trapping is a useful technique for detecting direct reactive oxygen species, such as superoxide (). However, the widely used spin trap 2,2-dimethyl-3,4-dihydro-2H-pyrrole N-oxide (DMPO) has several fundamental limitations in terms of half-life and stability. Recently, the new spin trap 2-diphenylphosphinoyl-2-methyl-3,4-dihydro-2H-pyrrole N-oxide (DPhPMPO) was developed by us. We evaluated the biological applicability of DPhPMPO to analyze in both cell-free and cellular systems. DPhPMPO had a larger rate constant for and formed more stable spin adducts for than DMPO in the xanthine/xanthine oxidase (X/XO) system. In the phorbol myristate acetate-activated neutrophil system, the detection potential of DPhPMPO for was significantly higher than that of DMPO (k_DMPO = 13.95 M⁻¹ s⁻¹, k_DPhPMPO = 42.4 M⁻¹ s⁻¹). These results indicated that DPhPMPO is a potentially good candidate for trapping in a biological system.     

Application of the Van Slyke-Cullen irreversible mechanism in the analysis of enzymatic progress curves

For enzymatic progress curves conforming to the Michaelis-Menten mechanism , the minimal fitting model cast as a system of numerically integrated differential equations is the simplified, irreversible Van Slyke-Cullen mechanism . The best-fit value of the bimolecular association rate constant is identical to the specificity constant k_cat/K_M. An illustrative example involves a fluorogenic continuous assay of the HIV protease, analyzed by the differential-equation oriented software package DYNAFIT [P. Kuzmic, Anal. Biochem. 237 (1996) 260].     

Theoretical investigation of the dissociative interchange (Id) mechanism for water exchange on magnesium(II) in aqueous solution

A dissociative (D) and a solvent-assisted dissociative interchange (I_d) water-exchange pathways for magnesium(II) in aqueous solution were simulated with density functional theory calculations. The D mechanism of includes a five-coordinated intermediate, while the I_d water-exchange pathway of proceeds with the assistance of a solvent water molecule, which supports the experimental assignment of the reaction mechanism. The intrinsic activation volume was used to differentiate between I_d and I_a mechanisms despite of the exclusion of the contribution of transmission coefficient. The calculated intrinsic activation volume for the I_d mechanism is consistent with the experimental data, and is closer to the experimental data than that for D mechanism. The I_d mechanism is suggested as the dominate water-exchange pathway of depending on the intrinsic activation volume with the assistance of the activation entropy. The calculations also showed that the influences of the explicit and bulk waters on energy barriers for D and I_d mechanisms are obviously different.     

Alkyl dehydrogenation in iridium tri-cyclopentyl phosphines

The iridium cyclooctadiene complex incorporating a tricyclopentyl phosphine ligand (PCyp₃), Ir(η²:η²-C₈H₁₂)(PCyp₃)Cl, has been prepared. Removal of the chloride from this complex using in CH₂Cl₂/arene solvent results in dehydrogenation (C-H activation followed by β-H transfer) of one of the alkyl phosphine rings and formation of the complexes (X = H, F) which contain a hybrid phosphine-alkene ligand. These complexes are formed alongside another product (5-20% yield) that has been identified as , which can be prepared in high yield by an alternative, and slightly modified, route. This complex is with a minor isomer that has been tentatively identified as , which results from allylic C-H activation of cyclooctadiene. Addition of H₂ to and its isomer in arene solvent (C₆H₅X, X = F, H) forms the dihydrido η⁶-arene Ir(III) complexes . In contrast, hydrogenation in CH₂Cl₂ alone results in the formation of in which the anion is now acting as a ligand through one of its aryl rings. The fluorobenzene complex can be cleanly converted to by addition of the hydrogen acceptor tert-butylethene (tbe).     

A trade-off relationship between energetic cost and entropic cost for in vitro evolution

In this paper, we consider two complementary cost functions for the landscape exploring processes to obtain the global optimum sequence through in vitro evolution protocol: one is the entropic cost C_etp, which is based on the deviation from the uniformity of a mutant distribution in sequence space, and the other is the energetic cost C_eng, which is based on the total number of sequences to be generated and evaluated. Based on a prior knowledge about the structure of a given fitness landscapes, the conductor of the experiment can think up the efficient search algorithm (ESA), which requires the minimum number of points (=sequences) to be searched up to the global optimum. For five typical fitness landscapes, we considered their respective (putative) ESA, and based on the ESA. As a result, we found a trade-off relationship between and for every case, that is, is approximately equal to the logarithm of the volume of the sequence space. and are interpreted in terms of the information-theoretic concepts.     

Evidence for intermediate S-states as initial phase in the process of oxygen-evolving complex oxidation

We have analyzed flash-induced period-four damped oscillation of oxygen evolution and chlorophyll fluorescence with the aid of a kinetic model of photosystem II. We have shown that, for simulation of the period-four oscillatory behavior of oxygen evolution, it is essential to consider the so-called intermediate S-state as an initial phase of each of the S_n-S_n+1, (n = 0, 1, 2, 3) transitions. The intermediate S-states are defined as []-states (n = 0, 1, 2, 3) and are formed with rate constant k_iSn ∼1.5 × 10⁶ s⁻¹, which was determined from comparison of theoretical predictions with experimental data. The assumed intermediate S-states shift the equilibrium in reaction more to the right and we suggest that kinetics of the intermediate S-states reflects a relaxation process associated with changes of the redox equilibrium in the above reaction. The oxygen oscillation is simulated without the miss and double-hit parameters, if the intermediate S-states, which are not the source of the misses or the double-hits, are included in the simulation. Furthermore, we have shown that the intermediate S-states, together with charge recombination, are prerequisites for the simulation of the period-four oscillatory behavior of the chlorophyll fluorescence.     

Kinetic studies of tris(2,2′-bipyridine)iron(III) perchlorate with cobaloxime, [Co(dmgBF2)2(H2O)2]

The kinetics of the reduction of by Co(dmgBF₂)₂(H₂O)₂ in 0.041 M HNO₃/NaNO₃ was found to be first-order in both the oxidizing and reducing agents and the second-order rate constant is given by k_obs = k₁ + k₂K[Cl⁻], with k₁=1.59 × 10⁶ M⁻¹ s⁻¹and k₂K = 1.83 × 10⁸ M⁻² s⁻¹, at 25 °C. The term that is first-order in [Cl⁻] is attributed to the formation of an ion-pair between and Cl⁻. For k₁, the activation parameters ΔH* and ΔS* are 2.22 ± 0.02 kcal mol⁻¹ and −22.7 ± 0.8 cal mol⁻¹ K⁻¹, respectively. The self-exchange rate constant of k₂₂ ≈ 8.7 × 10⁻³ M⁻¹ s⁻¹ for was estimated using Marcus theory and the known self-exchange rate constant for .     

Dinuclear gold(III) pyrazolato complexes - Synthesis, structural characterization and transformation to their trinuclear gold(I) and gold(I/III) analogues

The reaction of AuCl₃py with Na(pz∗) (pz∗ = pyrazolato, or substituted pyrazolato anion) yields stable dinuclear [cis-Au^IIICl₂(μ-pz∗)]₂ complexes. In the presence of a base, the latter undergo reduction with concomitant transformation of the dinuclear -structure to trinuclear Au^I, Au^III (containing trans Au^IIICl₂-centres) and species.     

Density-functional analysis of the electronic structure of tris-bipyridyl Ru(II) sensitisers

Excited state transitions and energies of a series of [Ru(bpy)₃]²⁺ type complexes incorporating the ligand, 4,4′-bis-phosphonato(methyl)-2,2′-bipyridine (dmpbpy) was investigated, and the influence of this organometallic ligand on the electronic structure of the complexes was examined using Time-Dependent Density Functional Theory (TD-DFT). Experimental data and the theoretical TD-DFT calculations were presented to support the effect of non-equivalent ligand substitution on spectral and molecular orbital (MO) energy properties on this class of tris-chelate surface sensitisers. For the series of complexes studied, it was identified that the lowest lying LUMO states were consistently found to reside on the ligand 2,2′-bipyridine (bpy) for gas phase calculations. As an implication of this, it was suggested that this could impact the effectiveness of these complexes as surface sensitisers in PEC cell applications such as the dye-sensitised solar cell (DSC) due to the lower probability of the excited state electron residing on a ligand anchored to the semiconductor substrate. However, further calculations in a solvation medium showed that the electron withdrawing nature of PO₃H₂ on dmpbpy saw the lowest lying LUMO states are populated on dmpbpy. This inhomogeneous distribution of electron density across non-equivalent ligands may have implications for further ‘spectral tuning’ of surface sensitisers. Despite the TD-DFT gas phase calculations not being corrected for solvent/media effects, the three longest wavelength bands associated with known charge transfer phenomena were identified. The symmetry allowed _MLCT in the visible region was assigned as a  ← dπ transition, the mid-UV spectrum _LC was assigned  ← π in origin. Whilst the near-UV shoulder on the blue side of _MLCT showed dσ ← dπ and π∗ ← dπ transitional character and was tentatively described as _MC/MLCT. UV-Vis absorption spectra calculated for solvated analogues containing dmpbpy indicated that the low energy transitions associated with the MLCT are subject to bathochromic shift due to solvent polarity by 0.062 eV (500 cm⁻¹) compared with the gas phase calculations, which is more highly correlated to the observed experimental transitions.     

Identification of the first steps in charge separation in bacterial photosynthetic reaction centers of Rhodobacter sphaeroides by ultrafast mid-infrared spectroscopy: electron transfer and protein dynamics

Time-resolved visible pump/mid-infrared (mid-IR) probe spectroscopy in the region between 1600 and 1800 cm⁻¹ was used to investigate electron transfer, radical pair relaxation, and protein relaxation at room temperature in the Rhodobacter sphaeroides reaction center (RC). Wild-type RCs both with and without the quinone electron acceptor Q_A, were excited at 600 nm (nonselective excitation), 800 nm (direct excitation of the monomeric bacteriochlorophyll (BChl) cofactors), and 860 nm (direct excitation of the dimer of primary donor (P) BChls (P_L/P_M)). The region between 1600 and 1800 cm⁻¹ encompasses absorption changes associated with carbonyl (CO) stretch vibrational modes of the cofactors and protein. After photoexcitation of the RC the primary electron donor P excited singlet state (P*) decayed on a timescale of 3.7 ps to the state (where B_L is the accessory BChl electron acceptor). This is the first report of the mid-IR absorption spectrum of ; the difference spectrum indicates that the 9-keto CO stretch of B_L is located around 1670-1680 cm⁻¹. After subsequent electron transfer to the bacteriopheophytin H_L in ∼1 ps, the state was formed. A sequential analysis and simultaneous target analysis of the data showed a relaxation of the radical pair on the ∼20 ps timescale, accompanied by a change in the relative ratio of the and bands and by a minor change in the band amplitude at 1640 cm⁻¹ that may be tentatively ascribed to the response of an amide CO to the radical pair formation. We conclude that the drop in free energy associated with the relaxation of , is due to an increased localization of the electron hole on the P_L half of the dimer and a further consequence is a reduction in the electrical field causing the Stark shift of one or more amide CO oscillators.     

Palladium-catalysed asymmetric allylation and complex formation involving P,N-bidentate diamidophosphites with 1,3,2-diazaphospholidine cycles

New chiral P,N-bidentate 1,3,2-diazaphospholidine ligands were obtained by one-step phosphorylation of (2S,3S)-2-(ferrocenylideneamino)-3-methylpentan-1-ol and (4S,5S)-(−)-2-methyl-4-hydroxymethyl-5-phenyl-2-oxazoline. Complexation of the new ligands with [Rh(CO)₂Cl]₂ and [Pd(allyl)Cl]₂ was found to give chelate complexes [Rh(CO)Cl(η²-P,N)] and , correspondingly. With the new P,N-ligands, up to 70% ee was achieved in the asymmetric Pd-catalysed sulfonylation of 1,3-diphenyl-2-propenyl acetate with sodium p-toluenesulfinate. In the enantioselective alkylation of 1,3-diphenyl-2-propenyl acetate with dimethyl malonate, up to 91% enantioselectivity was achieved by using complexes as chiral catalysts.     

Kinetic studies of the reduction of hexaaquacobalt(III) perchlorate by a cobaloxime, [Co(dmgBF2)2(H2O)2]

The reaction of with Co(dmgBF₂)₂(H₂O)₂ in 1.0 M HClO₄/LiClO₄ was found to be first-order in both reactants and the [H⁺] dependence of the second-order rate constant is given by k_2obs = b/[H⁺], b at 25 °C is 9.23 ± 0.14 × 10² s⁻¹. The [H⁺] dependence at lower temperatures shows some saturation effect that allowed an estimate of the hydrolysis constant for as K_a = 9.5 × 10⁻³ M at 10 and 15 °C. Marcus theory and the known self-exchange rate constant for Co(OH₂)₅OH^2+/+ were used to estimate an electron self-exchange rate constant of k₂₂ = 1.7 × 10⁻⁴ M⁻¹ s⁻¹ for .     

Kinetics and mechanism of the oxidation of oxalic acid by tetrachloroaurate(III) ion

The oxidation of oxalic acid by tetrachloroaurate(III) ion in 0.005 ? [HClO₄] ? 0.5 mol dm⁻³ is first order in and a fractional order in [oxalic acid], the reactive entities being AuCl₃(OH)⁻ and ions. The pseudo first-order rate, k_obs, with respect to [Au(III)], is retarded by increasing [H⁺] and [Cl⁻]. The retardation by H⁺ ion is caused by the dissociation equilibrium . A mechanism in which a substitution complex, is formed from AuCl₃(OH)⁻ and ions prior to its rate limiting disproportionation into products is suggested. The rate limiting constant, k, has been evaluated and its activation parameters are reported. The equilibrium constant K₁ for the formation of the substitution complex and its thermodynamic parameters are also reported.     

Kinetics and mechanism of the reaction between the di-μ-cyanobis[tetracyanoferrate(III)] complex ion and sulfite in aqueous solution

The kinetics of the stepwise reduction of the title complex [Fe₂(CN)₁₀]⁴⁻ by sulfite have been studied in the presence of air as a function of pH, sulfite concentration, temperature and ionic strength using stopped-flow and conventional spectrophotometric techniques. The k_obs versus pH profile shows a marked increase in rate with increase of pH over the range 3.7 ? pH ? 6.1 due to the increase in concentration of the more reactive sulfite species . The reaction proceeds in several stages, the first of which involves a one electron transfer process with the formation of the radical anion This then adds on in a rapid stage to form a species . The second and third stages also involve one electron transfer. In the third, or possibly a fourth stage cleavage occurs, the final product being [Fe^II(CN)₅(SO₃)]⁵⁻. The reaction rate is sensitive to the nature of the cation present with a reactivity sequence .