Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA

To characterize driving forces and driven processes in formation of a large-interface, wrapped protein-DNA complex analogous to the nucleosome, we have investigated the thermodynamics of binding the 34-base pair (bp) H′ DNA sequence to the Escherichia coli DNA-remodeling protein integration host factor (IHF). Isothermal titration calorimetry and fluorescence resonance energy transfer are applied to determine effects of salt concentration [KCl, KF, K glutamate (KGlu)] and of the excluded solute glycine betaine (GB) on the binding thermodynamics at 20 °C. Both the binding constant K_obs and enthalpy ΔH°_obs depend strongly on [salt] and anion identity. Formation of the wrapped complex is enthalpy driven, especially at low [salt] (e.g., ΔH^o_obs = − 20.2 kcal·mol^− 1 in 0.04 M KCl). ΔH°_obs increases linearly with [salt] with a slope (dΔH°_obs/d[salt]), which is much larger in KCl (38 ± 3 kcal·mol^− 1 M^− 1) than in KF or KGlu (11 ± 2 kcal·mol^− 1 M^− 1). At 0.33 M [salt], K_obs is approximately 30-fold larger in KGlu or KF than in KCl, and the [salt] derivative SK_obs = dlnK_obs/dln[salt] is almost twice as large in magnitude in KCl (− 8.8 ± 0.7) as in KF or KGlu (− 4.7 ± 0.6).A novel analysis of the large effects of anion identity on K_obs, SK_obs and on ΔH°_obs dissects coulombic, Hofmeister, and osmotic contributions to these quantities. This analysis attributes anion-specific differences in K_obs, SK_obs, and ΔH°_obs to (i) displacement of a large number of water molecules of hydration [estimated to be 1.0(± 0.2) × 10³] from the 5340 Å² of IHF and H′ DNA surface buried in complex formation, and (ii) significant local exclusion of F⁻ and Glu⁻ from this hydration water, relative to the situation with Cl⁻, which we propose is randomly distributed. To quantify net water release from anionic surface (22% of the surface buried in complexation, mostly from DNA phosphates), we determined the stabilizing effect of GB on K_obs: dlnK_obs/d[GB]  = 2.7 ± 0.4 at constant KCl activity, indicating the net release of ca. 150 H₂O molecules from anionic surface.     

Kinetics and thermodynamics of proton transfer to CpRu(dppe)H: Via dihydrogen bonding and (η-H2)-complex to the dihydride

The interaction between Cp^∗RuH(dppe) and a series of proton donors (HA) of increasing strength: CFH₂CH₂OH (MFE), CF₃CH₂OH (TFE), (CF₃)₂CHOH (HFIP), p-nitrophenol, CF₃COOH and HBF₄ has been investigated spectroscopically by variable-temperature IR, UV-Vis, and NMR spectroscopy in solvents of differing polarity (n-hexane, dichloromethane and their mixture). The low-temperature IR study shows the establishment of a hydrogen-bond which involves the hydride ligand as the proton accepting site. The basicity factor E_j for the hydride was found to be 1.39. All techniques indicate that an equilibrium exists between the dihydrogen-bonded complex and the cationic dihydrogen complex, [Cp^∗Ru(η²-H₂)(dppe)]⁺, the formation of which is shown here for the first time. The proton transfer from HFIP is characterized by ΔH^° = −8.1 ± 0.6 kcal mol⁻¹ and ΔS^° = −17 ± 3 eu. The activation parameters for the subsequent irreversible isomerization leading to the classical dihydride complex, [Cp^∗Ru(H)₂(dppe)]⁺, are ΔH^‡ = 20.9 ± 0.8 kcal mol⁻¹ and ΔS^‡ = 9 ± 3 eu as determined from ¹H NMR spectroscopy for protonation by HBF₄. Computational results at the DFT/B3PW91 level confirm the experimentally observed hydride basicity increase on descending the Group from iron to ruthenium and also the formation of the non-classical complex as an intermediate, prior to the thermodynamically favored dihydride.     

Kinetics and mechanism of the reduction of the molybdatopentaamminecobalt(III) ion by aqueous sulfite and aqueous potassium hexacyanoferrate(II)

A detailed investigation on the oxidation of aqueous sulfite and aqueous potassium hexacyanoferrate(II) by the title complex ion has been carried out using the stopped-flow technique over the ranges, 0.01≤[S(IV)]_T≤0.05 mol dm⁻³, 4.47≤pH≤5.12, and 24.9≤θ≤37.6 °C and at ionic strength 1.0 mol dm⁻³ (NaNO₃) for aqueous sulfite and 0.01≤[Fe(CN)₆ ⁴⁻]≤0.11 mol dm⁻³, 4.54≤pH≤5.63, and 25.0≤θ≤35.3 °C and at ionic strength 1.0 or 3.0 mol dm⁻³ (NaNO₃) for the hexacyanoferrate(II) ion. Both redox processes are dependent on pH and reductant concentration in a complex manner, that is, for the reaction with aqueous sulfite, k_obs={(k₁K₁K₂K₃+k₂K₁K₄[H⁺])[S(IV)]_T]/([H⁺]²+K₁[H⁺]+K₁K₂) and for the hexacyanoferrate(II) ion, k_obs={(k₁K₃K₄K₅+k₂K₃K₆[H⁺])[Fe(CN)₆ ⁴⁻]_T)/([H⁺]²+K₃[H⁺]+K₃K₄). At 25.0 °C, the value of k₁′ (the composite of k₁K₃) is 0.77±0.07 mol⁻¹ dm³ s⁻¹, while the value of k₂′ (the composite of k₂K₄) is (3.78±0.17)×10⁻² mol⁻¹ dm³ s⁻¹ for aqueous sulfite. For the hexacyanoferrate(II) ion, k₁′ (the composite of k₁K₅) is 1.13±0.01 mol⁻¹ dm³ s⁻¹, while the value of k₂′ (the composite of k₂K₆) is 2.36±0.05 mol⁻¹ dm³ s⁻¹ at 25.0 °C. In both cases there was reduction of the cobalt(III) centre to cobalt(II), but there was no reduction of the molybdenum(VI) centre. k₂₂, the self-exchange rate constant, for aqueous sulfite (as SO₃ ²⁻) was calculated to be 5.37×10⁻¹² mol⁻¹ dm³ s⁻¹, while for Fe(CN)₆ ⁴⁻, it was calculated to be 1.10×10⁹ mol⁻¹ dm³ s⁻¹ from the Marcus equations.     

Diastereomeric preference in 1,4,7-tris((S)-2-hydroxy-3-phenylpropyl)-1,4,7-triazacyclononanelithium(I) and its sodium(I) analogue

In N,N-dimethylformamide (DMF), 1,4,7-tris((S)-2-hydroxy-3-phenylpropyl)-1,4,7-triazacyclononane forms metal complexes, [M(S-thppc9)]⁺, for which log K (dm³ mol⁻¹)=3.01, 2.65, 2.66, 2.65, 2.42 and 7.59 (all±0.05) where M⁺=Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ and Ag⁺, respectively. Variable temperature ¹³C{¹H} NMR spectroscopy shows that the interchange between equivalent forms of a single diastereomer occurs for [Li(S-thppc9)]⁺ and [Na(S-thppc9)]⁺ characterised by: k=43±5 and 2900±100 s⁻¹, at 298.2 K, ΔH^‡=22.5±1.6 and 33.8±1.6 kJ mol⁻¹, and ΔS^‡=−133±5 and −59±6 J K⁻¹ mol⁻¹, respectively. Gas phase ab initio modelling shows these complexes and their K⁺ analogue to preferentially form distorted trigonal prismatic Λ, Δ, and Λ diastereomers, respectively.     

Interaction of meso-tetrakis (4-N-methylpyridyl) porphyrin in its free base and as a Zn(II) derivative with large unilamellar phospholipid vesicles

Our aim was to investigate the interaction of the cationic meso-tetrakis (4-N-methylpyridyl) porphyrin, a photosensitizer used for photodynamic therapy, in its free base form (TMPyP) and complexed with Zn(II) (ZnTMPyP), with large unilamellar vesicles (LUVs), as a model for the gram-negative bacterial cell wall. Mixtures of the zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG) phospholipids, at different molar percentages, were used as LUVs. A significant increase of porphyrin affinity at higher POPG molar concentrations was observed from the binding constant values, K _b, estimated by optical absorption and steady-state fluorescence. Besides, as demonstrated by time-resolved fluorescence, this affinity increase is also followed by a higher fraction of vesicle-bound porphyrin in the LUVs. Moreover, based on the K _b values, we have observed a higher affinity of the ZnTMPyP to the POPG containing LUVs as compared to the TMPyP. Steady-state fluorescence quenching and zeta potential studies revealed that both porphyrins are possibly located at the LUVs Stern layer region. Therefore, the electrostatic attraction between the positively charged porphyrin peripheral groups and the negatively charged outer surface of the LUVs plays an important role in porphyrin association and localization. Our results have improved the understanding of the successful application of cationic porphyrins on the photo-inactivation of gram-negative bacteria. Since a higher accumulation of the ZnTMPyP in the bacterial cell wall would be expected, this porphyrin could be a more efficient therapeutic drug for this treatment.     

Mechanistic studies on monodentate-ligand substitution of five-coordinate trigonal-bipyramidal platinum (II) complexes with tris[2-(diphenylphosphino)ethyl]phosphine

Reaction of the five-coordinate trigonal-bipyramidal platinum(II) complex, [Pt(pt)(pp₃)](BF₄) (pt = 1-propanethiolate, pp₃ = tris[2-(diphenylphosphino)ethyl]phosphine), with I⁻ in chloroform gave the five-coordinate square-pyramidal complex with a dissociated terminal phosphino group and an apically coordinated iodide ion in equilibrium. The thermodynamic parameters for the equilibrium between the trigonal-bipyramidal and square-pyramidal geometries, [Pt(pt)(pp₃)]⁺ + I⁻ ? [PtI(pt) (pp₃)], and the kinetic parameters for the chemical exchange were obtained as follows: , ΔH⁰ = − 10 ± 2.4 kJ mol⁻¹, ΔS⁰ = − 36 ± 10 J K⁻¹ mol⁻¹, , ΔH^‡ = 34 ± 4.7 kJ mol⁻¹, ΔS^‡ = − 50 ± 21 J K⁻¹ mol⁻¹. The square-planar trinuclear platinum(II) complex was formed by bridging reaction of one of the terminal phosphino groups of trigonal-bipyramidal [PtCl(pp₃)]Cl with trans-[PtCl₂(NCC₆H₅)₂] in chloroform. From these facts, ligand substitution reactions of [PtX(pp₃)]⁺ (X = monodentate anion) are expected to proceed via an intermediate with a dissociated phosphino group. The rate constants for the chloro-ligand substitution reactions of [PtCl(pp₃)]⁺ with Br⁻ and I⁻ in chloroform approached the respective limiting values as concentrations of the entering halide ions are increased. These kinetic results confirmed the preassociation mechanism in which the square pyramidal intermediate with a dissociated phosphino group and an apically coordinated halide ion is present in the rapid pre-equilibrium.     

Mixed-valency with cyanides as terminal ligands: Diruthenium(III,II) complexes with the 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine bridge and variable co-ligands (CN vs. bpy or NH3)

New diruthenium complexes (PPN)₄[(NC)₄Ru(μ-bptz)Ru(CN)₄], (PPN)₄1, and [(bpy)₂Ru(μ-bptz)Ru(CN)₄], 2, (PPN⁺ = bis(triphenylphospine)iminium; bptz = 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine; bpy = 2,2′-bipyridine), were synthesised and characterised by spectroscopic and electrochemical techniques. The comproportionation constant K_c = 10^7.0 of the mixed-valent species [(NC)₄Ru(μ-bptz)Ru(CN)₄]³⁻ as obtained by oxidation of 1⁴⁻ in CH₃CN is much lower than the K_c = 10^15.0 previously detected for [(H₃N)₄Ru(bptz)Ru(NH₃)₄]⁵⁺, reflecting the competition between CN⁻ and bptz for the π-electron density of the metals. Comparison with several other bptz-bridged diruthenium(II,III) complexes reveals an approximate correlation between K_c and the diminishing effective π acceptor capacity of the ancillary terminal ligands. In addition to the intense MLCT absorption at λ_max = 624 nm, the main IVCT (intervalence charge transfer) band of 1³⁻ was detected by spectroelectrochemistry at λ_max = 1695 nm (in CH₃CN; ε = 3200 M⁻¹ cm⁻¹). The experimental band width at half-height, Δν_1/2 = 2700 cm⁻¹, is slightly smaller than the theoretical value Δν_1/2 = 3660 cm⁻¹, calculated from the Hush approximation for Class II mixed-valent species. In agreement with comparatively moderate metal-metal coupling, the mixed-valent intermediate 1³⁻ was found to be EPR silent even at 4 K. The unsymmetrical mixed-valent complex [(bpy)₂Ru^II(μ-bptz)Ru^III(CN)₄]⁺, obtained in situ by bromine oxidation of 2 in CH₃CN/H₂O, displays a broad NIR absorption originating from an IVCT transition at λ_max = 1075 nm (ε ≈ 1000 M⁻¹ cm⁻¹, Δν_1/2 ≈ 4000 cm⁻¹). In addition, the lifetime of the excited-state of the mononuclear precursor complex [Ru(bptz)(CN)₄]²⁻ was measured in H₂O by laser flash photolysis; the obtained value of τ = 19.6 ns reveals that bptz induces a metal-to-ligand electronic delocalisation effect intermediate between that induced by bpy and bpz (bpz = 2,2′-bipyrazine) in analogous tetracyanoruthenium complexes.     

Energetic performance is improved by specific activation of K fluxes through KCa channels in heart mitochondria

Mitochondrial volume regulation depends on K⁺ movement across the inner membrane and a mitochondrial Ca²⁺-dependent K⁺ channel (mitoK_Ca) reportedly contributes to mitochondrial K⁺ uniporter activity. Here we utilize a novel K_Ca channel activator, NS11021, to examine the role of mitoK_Ca in regulating mitochondrial function by measuring K⁺ flux, membrane potential (ΔΨ_m), light scattering, and respiration in guinea pig heart mitochondria. K⁺ uptake and the influence of anions were assessed in mitochondria loaded with the K⁺ sensor PBFI by adding either the chloride (KCl), acetate (KAc), or phosphate (KH₂PO₄) salts of K⁺ to energized mitochondria in a sucrose-based medium. K⁺ fluxes saturated at ∼ 10 mM for each salt, attaining maximal rates of 172 ± 17, 54 ± 2.4, and 33 ± 3.8 nmol K⁺/min/mg in KCl, KAc, or KH₂PO₄, respectively. NS11021 (50 nM) increased the maximal K⁺ uptake rate by 2.5-fold in the presence of KH₂PO₄ or KAc and increased mitochondrial volume, with little effect on ΔΨ_m. In KCl, NS11021 increased K⁺ uptake by only 30% and did not increase volume. The effects of NS11021 on K⁺ uptake were inhibited by the K_Ca toxins charybdotoxin (200 nM) or paxilline (1 μM). Fifty nanomolar of NS11021 increased the mitochondrial respiratory control ratio (RCR) in KH₂PO₄, but not in KCl; however, above 1 μM, NS11021 decreased RCR and depolarized ΔΨ_m. A control compound lacking K_Ca activator properties did not increase K⁺ uptake or volume but had similar nonspecific (toxin-insensitive) effects at high concentrations. The results indicate that activating K⁺ flux through mitoK_Ca mediates a beneficial effect on energetics that depends on mitochondrial swelling with maintained ΔΨ_m.     

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 .     

Extraction properties for alkali metal picrates of macrocyclic trinuclear (p-cymene)ruthenium(II) and (pentamethylcyclopentadienyl)rhodium(III) complexes

The solvent extraction properties of macrocyclic trinuclear organometallic complexes, [(p-cymene)Ru(pyO₂)]₃ and [Cp^∗Rh(pyO₂)]₃, for Li⁺, Na⁺, and K⁺ picrates have been investigated in a dichloromethane-water system at 25 °C. The extraction rates of the alkali metal picrates with these macrocyclic complex ligands are unusually slow; the shaking times required to attain equilibrium are at least 1 h for [(p-cymene)Ru(pyO₂)]₃ and 20-40 h for [Cp^∗Rh(pyO₂)]₃. From analysis of the equilibrium data, the extraction constants (K_ex = [ML⁺A⁻]_o/[M⁺][L]_o[A⁻]; M⁺ = alkali metal ion, L = macrocyclic ligand, A⁻ = picrate ion, o = organic phase) have been determined. The log K_ex value varies in the sequences, Li⁺ (5.72) > Na⁺ (4.50) > K⁺ (2.88) for [(p-cymene)Ru(pyO₂)]₃ and Li⁺ (4.79) > Na⁺ (2.70) ≈ K⁺ (2.69) for [Cp^∗Rh(pyO₂)]₃. The K_ex values of 6,6-dibenzyl-14-crown-4 (DBz14C4), which is one of the best Li⁺-selective crown ethers, have also been determined for comparison. It is revealed that [Cp^∗Rh(pyO₂)]₃ is much superior to DBz14C4 both in the extractability for Li⁺ and the selectivity for Li⁺ over Na⁺.     

Interaction kinetics of liposome-incorporated unsaturated fatty acids with fatty acid-binding protein 3 by surface plasmon resonance

The role of heart-type fatty acid-binding protein (FABP3) in human physiology as an intracellular carrier of fatty acids (FAs) has been well-documented. In this study, we aimed to develop an analytical method to study real-time interaction kinetics between FABP3 immobilized on the sensor surface and unsaturated C18 FAs using surface plasmon resonance (SPR). To establish the conditions for SPR experiments, we used an FABP3-selective inhibitor 4-(2-(1-(4-bromophenyl)-5-phenyl-1H-pyrazol-3-yl)-phenoxy)-butyric acid. The affinity index thus obtained was comparable to that reported previously, further supporting the usefulness of the SPR-based approach for evaluating interactions between FABPs and hydrophobic ligands. A pseudo-first-order affinity of FABP3 to K⁺ petroselinate (C18:1 Δ6 cis), K⁺ elaidate (C18:1 Δ9 trans), and K⁺ oleate (C18:1 Δ9 cis) was characterized by the dissociation constant (K_d) near micromolar ranges, whereas K⁺ linoleate (C18:2 Δ9,12 cis/cis) and K⁺ α-linolenate (C18:3 Δ9,12,15 cis/cis/cis) showed a higher affinity to FABP3 with K_d around 1 × 10⁻⁶ M. Interactions between FAPB3 and C18 FAs incorporated in large unilamellar vesicles consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and FAs (5:1 molar ratio) were also analysed. Control DMPC liposomes without FA showed only marginal binding to FABP3 immobilized on a sensor chip while liposome-incorporated FA revealed significant responses in sensorgrams, demonstrating that the affinity of FAs to FABP3 could be evaluated by using the liposome-incorporated analytes. Significant affinity to FABP3 was observed for monounsaturated fatty acids (K_d in the range of 1 × 10⁻⁷ M). These experiments demonstrated that highly hydrophobic compounds in a liposome-incorporated form could be subjected to SPR experiments for kinetic analysis.     

Oxidation of thiocyanate by iron(V) in alkaline medium

The oxidation of thiocyanate by iron(V) (Fe(V)) was studied as a function of pH in alkaline solutions by a premix pulse radiolysis technique. The rates decrease with an increase in pH. The rate law for the oxidation of SCN⁻ by Fe(V) was obtained as −d[Fe(V)]/dt = k₁₀{[H⁺]²/([H⁺]² + K₂[H⁺] + K₂K₃)}[Fe(V)][SCN⁻], where k₁₀ = 5.72 ± 0.19 × 10⁶ M⁻¹ s⁻¹, pK₂ = 7.2, and pK₃ = 10.1. The reaction precedes via a two-electron oxidation, which converts Fe(V) to Fe(III). Thiocyanate reacts approximately 10³× faster with iron(V) than does with iron(VI).     

The kinetics of the complex formation between iron(III)-ethylenediaminetetraacetate and hydrogen peroxide in aqueous solution

The kinetics of the formation of the purple complex [Fe^III(EDTA)O₂]³⁻, between Fe^III-EDTA and hydrogen peroxide was studied as a function of pH (8.22-11.44) and temperature (10-40 °C) in aqueous solutions using a stopped-flow method. The reaction was first-order with respect to both reactants. The observed second-order rate constants decrease with an increase in pH and appear to be related to deprotonation of Fe^III-EDTA ([Fe(EDTA)H₂O]⁻ ⇔ Fe(EDTA)OH]²⁻ + H⁺). The rate law for the formation of the complex was found to be d[Fe^IIIEDTAO₂]³⁻/dt=[(k₄[H⁺]/([H⁺] + K₁)][Fe^III-EDTA][H₂O₂], where k₄=8.15±0.05×10⁴ M⁻¹ s⁻¹ and pK₁=7.3. The steps involved in the formation of [Fe(EDTA)O₂]³⁻ are briefly discussed.     

Homogeneous oxidative coupling catalysts. Mechanism of catalysts formation by oxidation of [(Pip)nCuX]4 (n = 1 or 2, Pip = piperidine, X = Cl, Br or I) by dioxygen in aprotic media

This paper reports the mechanism of formation of oxidative coupling catalysts [(Pip)_nCuX]₄O₂, n = 1 or 2 and X = Cl, Br or I, which represent half of the catalytical cycle, Scheme 1. The mechanism has been described as a pre-equilibrium between [(Pip)_nCuX]₄ and O₂. K values are very sensitive to how strong the hydrogen-bonding between copper (I) tetranuclear and incoming dioxygen is, such association is also sensitive to the variation of X. The pronounced pre-equilibrium is the reason behind the oxidation of [(Pip)_nCuI]₄, which is not the case for pyridine type of ligands. The pre-equilibrium followed by rate determining step k₂, which is responsible to the formation of the oxidative coupling catalysts [(Pip)_nCuX]₄O₂. The overall reaction is a second-order process, first order in each [[(Pip)_nCuX]₄] and [O₂], with rate constant k_on (k_on = Kk₂) and exothermic ΔH^≠ varying from −3 to −12 kcal mol⁻¹ and ΔS^≠ varying from −87 to −65 cal deg⁻¹ mol⁻¹. k_on were found to be very sensitive to n value 1 or 2 and to the type of X (Cl, Br or I).     

Bcl-2 Promoter Sequence G-Quadruplex Interactions with Three Planar and Non-Planar Cationic Porphyrins: TMPyP4, TMPyP3, and TMPyP2

The interactions of three related cationic porphyrins, TMPyP4, TMPyP3 and TMPyP2, with a WT 39-mer Bcl-2 promoter sequence G-quadruplex were studied using Circular Dichroism, ESI mass spectrometry, Isothermal Titration Calorimetry, and Fluorescence spectroscopy. The planar cationic porphyrin TMPyP4 (5, 10, 15, 20-meso-tetra (N-methyl-4-pyridyl) porphine) is shown to bind to a WT Bcl-2 G-quadruplex via two different binding modes, an end binding mode and a weaker mode attributed to intercalation. The related non-planar ligands, TMPyP3 and TMPyP2, are shown to bind to the Bcl-2 G-quadruplex by a single mode. ESI mass spectrometry experiments confirmed that the saturation stoichiometry is 4:1 for the TMPyP4 complex and 2:1 for the TMPyP2 and TMPyP3 complexes. ITC experiments determined that the equilibrium constant for formation of the (TMPyP4)₁/DNA complex (K₁ = 3.7 × 10⁶) is approximately two orders of magnitude greater than the equilibrium constant for the formation of the (TMPyP2)₁/DNA complex, (K₁ = 7.0 × 10⁴). Porphyrin fluorescence is consistent with intercalation in the case of the (TMPyP4)₃/DNA and (TMPyP4)₄/DNA complexes. The non-planar shape of the TMPyP2 and TMPyP3 molecules results in both a reduced affinity for the end binding interaction and the elimination of the intercalation binding mode.     

Nitrilotris(methylenephosphonates) in aqueous solution and solid state - dilatometric, potentiometric and NMR investigations

Dissociation and alkali complex formation equilibria of nitrilotris(methylenephosphonic acid) (NTMP, H₆L) have been studied by dilatometric, potentiometric and ³¹P NMR-controlled titrations. Dilatometry indicated the formation of alkali complexes ML (M=Li, Na, K, Rb, Cs) at high pH with a stability decreasing from Li to Cs. An efficient combination of potentiometric and NMR methods confirmed two types of alkali metal complexes MHL and ML. Stability constants for the equilibria following M⁺ + HL⁵⁻ ? MHL⁴⁻ and M⁺ + L⁶⁻ ? ML⁵⁻, respectively, were determined: logK_NaHL=1.08(0.07), logK_KHL=0.86(0.08), logK_NaL=2.24(0.03). Systematic errors are introduced by using alkali metal hydroxides as titrants for routine potentiometric determinations of dissociation constants pK_a5^app and pK_a6^app. Correction formulae were derived to convert actual dissociation constants pK_a into apparent dissociation constants pK_a^app (or vice versa). The actual dissociation constants were found: pK_a5(H₂L⁴⁻ ? H⁺ + HL⁵⁻)=7.47(0.03) and pK_a6(HL⁵⁻ ? H⁺ + L⁶⁻)=14.1(0.1). The anisotropy of ³¹P chemical shifts of salts M_nH_6 − nL (M=Li, Na, n=0-5) is more sensitive towards titration (n) than isotropic solution state chemical shifts.     

Kinetics study of the substitution reaction of fac-[Fe(CN)2(CO)3I] with PPh3

Substitution reaction of fac-[Fe^II(CN)₂(CO)₃I]⁻ with triphenylphosphine (PPh₃) produced mono phosphine substituted complex cis-cis-[Fe^II(CN)₂(CO)₂(PPh₃)I]⁻. Crystal structure of the product showed that carbonyl positioned trans- to iodide was replaced by PPh₃. The substitution reaction was monitored by quantitative infrared spectroscopic method, and the rate law for the substitution reaction was determined to be rate = k[[Fe^II(CN)₂(CO)₂(PPh₃)I]⁻][PPh₃]. Transition state enthalpy and entropy changes were obtained from Eyring equation k = (k_BT/h)exp(−ΔH^≠/RT + ΔS^≠/R) with ΔH^≠ = 119(4) kJ mol⁻¹ and ΔS^≠ = 102(10) J mol⁻¹ K⁻¹. Positive transition state entropy change suggests that the substitution reaction went through a dissociative pathway.     

Ionic microenvironmental effects on triplex DNA stabilization: Cationic counterion effects on poly(dT)·poly(dA)·poly(dT)

The structure and conformation of nucleic acids are influenced by metal ions, polyamines, and the microenvironment. In poly(purine) · poly(pyrimidine) sequences, triplex DNA formation is facilitated by metal ions, polyamines and other ligands. We studied the effects of mono- and di-valent metal ions, and ammonium salts on the stability of triple- and double-stranded structures formed from poly(dA) and poly(dT) by measuring their respective melting temperatures. In the presence of metal ions, the absorbance versus temperature profile showed two transitions: T_m1 for triplex to duplex and single stranded DNA, and T_m2 for duplex DNA melting to single stranded DNA. Monovalent cations (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ and ₄NH⁺${{\text{NH}}_4}^{+}$) promoted triplex DNA at concentrations ≥150 mM. T_m1 varied from 49.8 °C in the presence of 150 mM Li⁺ to 30.6 °C in the presence of 150 mM K⁺. ₄NH⁺${{\text{NH}}_4}^{+}$ was very effective in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with methyl, ethyl, propyl and butyl groups. As in the case of monovalent cations, a concentration-dependent increase in T_m1 was observed with divalent ions and triplex DNA stabilization decreased in the order: Mg²⁺ > Ca²⁺ > Sr²⁺ > Ba²⁺. All positively charged cations increased the melting temperature of duplex DNA. Values of Δn (number of ions released) on triplex DNA melting were 0.46 ± 0.06 and 0.18 ± 0.02, respectively, for mono- and di-valent cations, as calculated from 1/T_m1 versus ln[M^+,2+] plots. The corresponding values for duplex DNA were 0.25 ± 0.02 and 0.12 ± 0.02, respectively, for mono- and di-valent cations. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. Our results might be useful in developing triplex forming oligonucleotide based gene silencing techniques.     

An improved synthesis, crystal structures, and metallochromism of salts of [Ru(tolyl-terpy)(CN)3]

The previously reported complex [Ru(ttpy)(CN)₃]⁻ [ttpy = 4′(p-tolyl)-2,2′:6′,2″-terpyridine] is conveniently synthesised by reaction of ttpy with Ru(dmso)₄Cl₂ to give [Ru(ttpy)(dmso)Cl₂], which reacts in turn with KCN in aqueous ethanol to afford [Ru(ttpy)(CN)₃]⁻ which was isolated and crystallographically characterised as both its (PPN)⁺ and K⁺ salts. The K⁺ salt contains clusters containing three complex anions and three K⁺ cations connected by end-on and side-on cyanide ligation to the K⁺ ions. The solution speciation behaviour of [Ru(ttpy)(CN)₃]⁻ was investigated with both Zn²⁺ and K⁺ salts in MeCN, a solvent sufficiently non-competitive to allow the added metal cations to associate with the complex anion via the externally-directed cyanide lone pairs. UV-Vis spectroscopic titration of (PPN)[Ru(ttpy)(CN)₃] with Zn(ClO₄)₂ showed a blue shift of 2900 cm⁻¹ in the ¹MLCT absorption manifold due to the ‘metallochromism’ effect; a series of distinct binding events could be discerned corresponding to formation of 4:1, 1:1 and then 1:3 anion:cation adducts, all with high formation constants, as the titration proceeded. In contrast titration of (PPN)[Ru(ttpy)(CN)₃] with the more weakly Lewis-acidic KPF₆ resulted in a much smaller blue-shift of the ¹MLCT absorptions, and the titration data corresponded to formation of 1:1 and then 2:1 cation:anion adducts with weaker stepwise association constants of the order of 10⁴ and then 10³ M⁻¹. Although association of [Ru(ttpy)(CN)₃]⁻ resulted in a blue-shift of the ¹MLCT absorptions, the luminescence was steadily quenched, as raising the ³MLCT level makes radiationless decay via a low-lying ³MC state possible.     

Cyanide and chloride exchange on homoleptic gold(III) square-planar complexes: variable pressure kinetic investigation by heteronuclear NMR

Kinetic studies of X⁻ exchange on [AuX₄]⁻ square-planar complexes (where X=Cl⁻ and CN⁻) were performed at acidic pH in the case of chloride system and as a function of pH for the cyanide one. Chloride NMR study (330-365 K) gives a second-order rate law on [AuCl₄]⁻ with the kinetic parameters: (k₂^Au,Cl)²⁹⁸=0.56±0.03 s⁻¹ mol⁻¹ kg; ΔH₂^‡ Au,Cl=65.1±1 kJ mol⁻¹; ΔS₂^‡ Au,Cl=−31.3±3 J mol⁻¹ K⁻¹ and ΔV₂^‡ Au,Cl=−14±2 cm³ mol⁻¹. The variable pressure data clearly indicate the operation of an I_a or A mechanism for this exchange pathway. The proton exchange on HCN was determined by ¹³C NMR as a function of pH and the rate constant of the three reaction pathways involving H₂O, OH⁻ and CN⁻ were determined: k₀^HCN,H=113±17 s⁻¹, k₁^HCN,H=(2.9±0.7)×10⁹ s⁻¹ mol⁻¹ kg and k₂^HCN,H=(0.6±0.2)×10⁶ s⁻¹ mol⁻¹ kg at 298.1 K. The rate law of the cyanide exchange on [Au(CN)₄]⁻ was found to be second order with the following kinetic parameters: (k₂^Au,CN)²⁹⁸=6240±85 s⁻¹ mol⁻¹ kg, ΔH₂^‡ Au,CN=40.0±0.8 kJ mol⁻¹, ΔS₂^‡ Au,CN=−37.8±3 J mol⁻¹ K⁻¹ and ΔV₂^‡ Au,CN=+2±1 cm³ mol⁻¹. The rate constant observed varies about nine orders of magnitude depending on the pH and HCN does not act as a nucleophile. The observed rate constant of X⁻ exchange on [AuX₄]⁻ are two or three orders of magnitude faster than the Pt(II) analogue.