Marcus treatment of endergonic reactions: a commentary

Two forms of the equation for expression of the rate constant for electron transfer through a Marcus-type treatment are discussed. In the first (exergonic) form, the Arrhenius exponential term was replaced by its classical Marcus term; in the second (endergonic) form, the forward rate constant was replaced by the reverse rate constant (the forward rate constant in the exergonic direction), which was expanded to an equivalent Marcus term and multiplied by the equilibrium constant. When the classical Marcus treatment was used, these two forms of the rate equation give identical curves relating the logarithm of the rate constant to the driving force. The Marcus term for the relation between activation free-energy, DeltaG#, reorganization energy, lambda, and driving force, DeltaG(o), derived from parabolas for the reactant and product states, was identical when starting from exergonic or endergonic parabolas. Moser and colleagues introduced a quantum mechanical correction factor to the Marcus term in order to fit experimental data. When the same correction factor was applied in the treatment for the endergonic direction by Page and colleagues, a different curve was obtained from that found with the exergonic form. We show that the difference resulted from an algebraic error in development of the endergonic equation.     

Effects of Temperature and ΔG° on Electron Transfer from Cytochrome c2 to the Photosynthetic Reaction Center of the Purple Bacterium Rhodobacter sphaeroides

The kinetics of electron transfer from cytochrome c₂ to the primary donor (P) of the reaction center from the photosynthetic purple bacterium Rhodobacter sphaeroides have been investigated by time-resolved absorption spectroscopy. Rereduction of P⁺ induced by a laser pulse has been measured at temperatures from 300 K to 220 K in a series of specifically mutated reaction centers characterized by altered midpoint redox potentials of P⁺/P varying from 410 mV to 765 mV (as compared to 505 mV for wild type). Rate constants for first-order electron donation within preformed reaction center–cytochrome c₂ complexes and for the bimolecular oxidation of free cytochrome c₂ have been obtained by multiexponential deconvolution of the kinetics. At all temperatures the rate of the fastest intracomplex electron transfer increases by more than two orders of magnitude as the driving force −ΔG° is varied over a range of 350 meV. The temperature and ΔG° dependences of the rate constant fit the Marcus equation well. Global analysis yields a reorganization energy λ = 0.96 ± 0.07 eV and a set of electronic matrix elements, specific for each mutant, ranging from 1.2 10⁻⁴ eV to 2.5 10⁻⁴ eV. Analysis in terms of the Jortner equation indicates that the best fit is obtained in the classical limit and restricts the range of coupled vibrational modes to frequencies lower than ∼200 cm⁻¹. An additional slower kinetic component of P⁺ reduction, attributed to electron transfer from cyt c₂ docked in a nonoptimal configuration of the complex, displays a Marcus type dependence of the rate constant upon ΔG°, characterized by a similar value of λ (0.8 ± 0.1 eV) and by an average electronic matrix element smaller by more than one order of magnitude. In all of the mutants, as the temperature is decreased below 260 K, both intracomplex reactions are abruptly inhibited, their rate being negligible at 220 K. The free energy dependence of the second-order rate constant for oxidation of cyt c₂ in solution suggests that the collisional reaction is partially diffusion controlled, reaching the diffusion limit at exothermicities between 150 and 250 meV over the temperature range investigated.     

Steric effects on activation energy for the electrochemical oxidation of organocobaloximes

Heterogeneous electron transfer rate constants were determined as a function of electrode potential for one-electron oxidation in acetonitrile (AN) at O °C of a series of organocobaloximes [R-Co(DH)₂L] bearing widely different organic groups. Reaction entropies were determined by voltammetric half-wave potential (E^r_{$\text{1}\text{2}$}) measurements in a non-isothermal cell. The electron transfer coefficients and reorganization parameters were calculated following the Marcus theory. The reaction free energies relative to a reference couple ΔG° are linearly correlated with the polar Taft constant of the organic substituent R.The steric effects on ΔG° are shown by the correlation of E^r_{$\text{sol1}\text{2}$} with the CoC bond distance.Assuming constancy of double layer effects along the series in the given solution composition, the trends of the apparent rate constants k_app were considered in order to evaluate the effects of the nature of the organic ligand on the activation energy ΔG³ of the electron transfer. The steric effects on ΔG³ are pointed out i.a. by consideration of the relationship between ΔG³ and ΔG°.     

The use of rotating disk voltammetry for the determination of homogeneous small molecule--redox protein reaction rates

Rotating disk voltammetry was used in this work to study the rates of reaction of ferricytochrome c with two very strong reductants, methyl and benzyl viologen. The rates of reaction for these reductants were found to be 4.0 × 10⁷ and 5.4 × 10⁷m^?1s^?1 at 24°C for benzyl and methyl viologen, respectively. The versatility of this method was demonstrated by the ease with which the activation parameters were obtained. The ΔH^≠ and ΔS^≠ were found to be 4.0 kcal/mol and ?10.6 cal/mol-K, respectively, for benzyl viologen. All the observed reaction rates were corrected for coulombic effects by the method of Wherland and Gray, and the electrostatically corrected rate constants were compared with the Marcus and Hopfield theories for electron transfer. The agreement was excellent for the tunneling theory but there were some discrepancies with the absolute Marcus theory. The relative Marcus approach worked quite well and, by taking into account the nonadiabaticity of the electron transfer, reasonable values were obtained for the absolute Marcus theory when realistic values of the self-exchange constants were used.     

Limited reversibility of transmembrane proton transfer assisting transmembrane electron transfer in a dihaem-containing succinate:quinone oxidoreductase

Membrane protein complexes can support both the generation and utilisation of a transmembrane electrochemical proton potential (Δp), either by supporting transmembrane electron transfer coupled to protolytic reactions on opposite sides of the membrane or by supporting transmembrane proton transfer. The first mechanism has been unequivocally demonstrated to be operational for Δp-dependent catalysis of succinate oxidation by quinone in the case of the dihaem-containing succinate:menaquinone reductase (SQR) from the Gram-positive bacterium Bacillus licheniformis. This is physiologically relevant in that it allows the transmembrane potential Δp to drive the endergonic oxidation of succinate by menaquinone by the dihaem-containing SQR of Gram-positive bacteria. In the case of a related but different respiratory membrane protein complex, the dihaem-containing quinol:fumarate reductase (QFR) of the ?-proteobacterium Wolinella succinogenes, evidence has been obtained that both mechanisms are combined, so as to facilitate transmembrane electron transfer by proton transfer via a both novel and essential compensatory transmembrane proton transfer pathway (“E-pathway”). Although the reduction of fumarate by menaquinol is exergonic, it is obviously not exergonic enough to support the generation of a Δp. This compensatory “E-pathway” appears to be required by all dihaem-containing QFR enzymes and results in the overall reaction being electroneutral. However, here we show that the reverse reaction, the oxidation of succinate by quinone, as catalysed by W. succinogenes QFR, is not electroneutral. The implications for transmembrane proton transfer via the E-pathway are discussed.     

Kinetics of selenite uptake by mononuclear cells from peripheral human blood

The present study deals with the kinetics and thermodynamics of the uptake of⁷⁵Se-labeled SeO ₃ ^2? from incubation media to lymphocytes cultivated from eight normal individuals (14–55 years of age, two females). The uptake of SeO ₃ ^2? was evaluated on the assumption of pseudo-first-order kinetics with regard to a reacting cellular receptor pool. On the basis of the experimental observations, it was assumed that the suggested pool of receptor molecules-symbolically represented by “£H₄”—reacts with SeO ₃ ^2? in the hypothetical reaction: $$\pounds H_4 + SeO_3^{2 - } + 2H^ + \underset{{ - k_1 }}{\overset{{k_1 }}{\longleftrightarrow}}\pounds Se + 3H_2 O$$ The mean value of the change in standard free energy at 25°C was calculated to be ΔG ^o=?141.6±1.3 kJ/mol, while the corresponding mean value of the free energy of activation at 25°C was calculated to be ΔG ²⁺=?7.8±0.9 kJ/mol for the forward reaction. The calculated values of the corresponding individual changes in the respective standard enthalpies and entropies were mutually interdependent for all eight donors. ΔH ^o=?152+315ΔS ^o(kJ/mol) corresponding to the common value ΔG ^o??152 kJ/mol at 315°K. These mutual interdependencies are possibly the effect of variable conformational states (e.g., the macromolecular compactness) of the cellular receptor pools. This suggestion may furthermore be supported by the correlation traced between ΔH ^o vs the biological age in years of the donors: △H ^°?76.7?1.0 (age)kJ/mol (r = ?0.92) The calculated values of activation enthalpy ΔH ²⁺ kJ/mol and activation entropy ΔS ²⁺ (kJ/mol K) also mutually correlated linearly (r=0.998); the regression line was: △H ²⁺ = ?8.9 + 305△S²⁺ (kJ/mol) corresponding to the common value △H ²⁺ △ ?8.9 (kJ/mol) at 305°K Similarly the activation enthalpy ΔH ²⁺ vs the biological age in years correlated linearly: ΔH ²⁺=67.4?0.73(age) (kJ/mol) (r=?0.76) The range of ΔH ²⁺ studied was from 13.8 to 53.9 kJ/mol with a linearly corresponding range in ΔS ²⁺ from 73 to 205 J/mol K. The thermodynamic data reveal the selenite uptake during the hypothetical standard reaction to be exergonic and endothermic. Critical pH dependencies of the selenite uptake were explained.     

Quantitative estimates of steric effects: Intramolecular strain energy effects on the activation energy for aquation of some trans-dichlorotetraaminecobalt(III) complexes

In an effort to quantitatively estimate steric contributions to the aquation rates of a series of structurally related cobalt(III) tetraamine complexes, strain energy minimization calculations have been performed on the reactant and some plausible transition state structures. Free energies of activation ΔG*_obs, are factored as: ΔG*_obs, = ΔG*_bb + ΔG*_strain + Δ_G*_CF + ΔG*_solvation + … where ΔG*_bb is the free energy change associated with bond breaking, ΔG*_solvation is the solvation free energy difference between the reactant and a proposed transition stare, ΔG*_CF is the difference in crystal field stabilization between the reactant and a proposed transition state, and ΔG*_strain is the strain energy difference between the reactant complex and a proposed transition state. The activation energy for the aquation of a hypothetical ‘strain free’ complex is defined as ΔG*_int and reflects the energy required for the bond breaking step with all other terms. For the cations trans-(RR,SS)-dichloro-1,8- diamino-3,6-diazaoctanecobalt(III)(trans [Co(2,2,2- tet)Cl₂]⁺), trans-(RR,SS)- or trans-(RS)-dichloro-1.9- diamino-3,7-diazanonanecobalt(III)(trans [Co(2,3,2- tet)Cl₂]⁺ and trans-(RS)-dichloro-1,10-diamino-4,7- diazadecanecobalt(III)(trans[Co(3,2,3-tet)Cl₂]⁺) ΔG*_int is found to be a constant 123 kJ/mol. For the trans-dichlorocobalt(III) complexes with the ligands 1,4,7,10-tetraazacyclotridecane([13]-ane-N₄), 1,4,8, 11-tetraazacyclotetradecane([14]-ane-N₄), 1,4,8,12- tetraazacyclopentadecane([15]-ane-N₄) and 1,5,9,13- tetraazacyclohexadecane([16]-ane-N₄), ΔG*_int lies in the range 133–139 kJ/mol.     

Theoretical study on the mechanism of catalytic reduction of hydrazine to ammonia mediated by vanadium (III) thiolate complexes

DFT calculations on the free energy profile for the catalytic reduction of hydrazine to ammonia, the late stage of nitrogen fixation, mediated by vanadium (III) thiolate complexes VPS3 (1) and VNS3 (7) were carried out. The calculated energy profile revealed that all the reduction steps were exergonic while the protonation steps were endergonic. The generation of first equivalent of ammonia and the reduction of the cationic complex [V-NH₃]⁺ to the neutral V-NH₃ species were found to be the most exergonic of all the steps. Based on the calculated energy profile, both VPS3 and VNS3 were found to be catalytically active for the reduction of hydrazine to ammonia, although some quantitative differences in free energy profile had been observed.     

Isokinetic Relationship in the Oxidation of Cuprous Stellacyanin by Cobalt(III) Complexes

Rate parameters have been obtained for the oxidation of cuprous stellacyanin by cobalt(III) ions of the form cis(N)-[CoN₂O₄]^?, including cis(N)-[Co(NTA)(gly)]^?, cis(N)-[Co(IDA)₂]^?, [Co(en)(ox)₂]^?(μ 0.5 M(phosphate), pH 7.0), and Co(EDTA)^?(μ 0.1 M(NaCl), pH 7.2, 0.001 M phosphate). An excellent isokinetic correlation between the activation parameters ΔH^≠ and ΔS^≠ exists for the reactions of aminopolycarboxylatocobalt(III) ions with reduced stellacyanin (β = 300 ± 12 K; correlation coefficient = 0.995). It is concluded that enthalpy-entropy compensation in these reactions may be understood in terms of differing orientations preferred by the various oxidants in forming precursor complexes with the reduced blue protein. While ΔH^≠ and ΔS^≠ values for electron transfer from stellacyanin to cis(N)-[CoN₂O₄]^? ions vary over ranges of 10.7 kcal/mol and 34 cal/mol-deg, respectively, room temperature rate constants are relatively constant (3.6–34.5 M^?1 sec^?1), as expected from Marcus theory for outer sphere electron transfer.     

IGERS: Inferring Gibbs Energy Changes of Biochemical Reactions from Reaction Similarities

Mathematical analysis and modeling of biochemical reaction networks requires knowledge of the permitted directionality of reactions and membrane transport processes. This information can be gathered from the standard Gibbs energy changes (ΔG⁰) of reactions and the concentration ranges of their reactants. Currently, experimental ΔG⁰ values are not available for the vast majority of cellular biochemical processes. We propose what we believe to be a novel computational method to infer the unknown ΔG⁰ value of a reaction from the known ΔG⁰ value of the chemically most similar reaction. The chemical similarity of two arbitrary reactions is measured by the relative number (T) of co-occurring changes in the chemical attributes of their reactants. Testing our method across a validated reference set of 173 biochemical reactions with experimentally determined ΔG⁰ values, we found that a minimum reaction similarity of T = 0.6 is required to infer ΔG⁰ values with an error of <10 kJ/mol. Applying this criterion, our method allows us to assign ΔG⁰ values to 458 additional reactions of the BioPath database. We believe our approach permits us to minimize the number of ΔG⁰ measurements required for a full coverage of a given reaction network with reliable ΔG⁰ values.     

Hexavalent chromium removal from aqueous solution by adsorption on treated sawdust

The studies on adsorption of hexavalent chromium were conducted by varying various parameters such as contact time, pH, amount of adsorbent, concentration of adsorbate and temperature. The kinetics of adsorption of Cr(VI) ion followed pseudo second order. Langmuir adsorption isotherm was employed in order to evaluate the optimum adsorption capacity of the adsorbent. The adsorption capacity was found to be pH dependant. Sawdust was found to be very effective and reached equilibrium in 3 h (adsorbate concentration 30 mg l⁻¹). The rate constant has been calculated at 303, 308, 313 and 318 K and the activation energy (E_a) was calculated using the Arrhenius equation. Thermodynamic parameters such as standard Gibbs energy (ΔG°) and heat of adsorption (ΔH_r) were calculated. The ΔG° and ΔH_r values for Cr(VI) adsorption on the sawdust showed the process to be exothermic in nature. The percentage of adsorption increased with decrease in pH and showed maximum removal of Cr(VI) in the pH range 4.5–6.5 for an initial concentration of 5 mg l⁻¹.     

Investigations on purine and pyrimidine bases stacking associations in aqueous solutions by the fluorescence quenching method: I. Autoassociation of 2-aminopurine

A general equation was derived, describing fluorescence quantum yield and lifetime of an autoassociating compound in liquid solutions. The autoassociation of 2-aminopurine in aqueous solution was examined within the range from 0 to 90°C. The compound seemed to associate cooperatively. The thermodynamic parameters of polymerization change with temperature, so that its free enthalpy ΔG = ?0.0797 T² + 45.4 T ?7893. The dimerization enthalpy and entropy are approximately temperature-independent (ΔH₂ = ?4.17 $\text{kcal}\text{mol}$, ΔS₂ = ?10.9 e.u.), although the function: ΔG₂ = ?0.0308 T² + 30.3 T - 7213 fits experimental points better. The observed dependences can be explained by the increasing role of the hydrophobic effect with temperature and size of the aggregates. The association rate constants were determined, and a two-step reaction mechanism was demonstrated. The first step is diffusion-controlled. The second is characterized by an activation energy of ~2 $\text{kcal}\text{mol}$ and an encounter distance of ~8.3 Å.     

The ins and outs of Na bioenergetics in Acetobacterium woodii

The acetogenic bacterium Acetobacterium woodii uses a transmembrane electrochemical sodium ion potential for bioenergetic reactions. A primary sodium ion potential is established during carbonate (acetogenesis) as well as caffeate respiration. The electrogenic Na⁺ pump connected to the Wood-Ljungdahl pathway (acetogenesis) still remains to be identified. The pathway of caffeate reduction with hydrogen as electron donor was investigated and the only membrane-bound activity was found to be a ferredoxin-dependent NAD⁺ reduction. This exergonic electron transfer reaction may be catalyzed by the membrane-bound Rnf complex that was discovered recently and is suggested to couple exergonic electron transfer from ferredoxin to NAD⁺ to the vectorial transport of Na⁺ across the cytoplasmic membrane. Rnf may also be involved in acetogenesis. The electrochemical sodium ion potential thus generated is used to drive endergonic reactions such as flagellar rotation and ATP synthesis. The ATP synthase is a member of the F₁F_O class of enzymes but has an unusual and exceptional feature. Its membrane-embedded rotor is a hybrid made of F_O and V_O-like subunits in a stoichiometry of 9:1. This stoichiometry is apparently not variable with the growth conditions. The structure and function of the Rnf complex and the Na⁺ F₁F_O ATP synthase as key elements of the Na⁺ cycle in A. woodii are discussed.     

Evidence for a high proton translocation stoichiometry of the H+-ATPase complex in well coupled proteoliposomes reconstituted from a thermophilic cyanobacterium

Evidence is presented for a high proton translocation stoichiometry (H+/ATP) of approx. 9 in ATPase proteoliposomes with extremely low permeability for ions, reconstituted from a thermophilic cyanobacterium. A proportional relation between the phosphate potential (ΔG_fp) and the proton-motive force (Δp) was observed in thermodynamic equilibrium. A bulk-to-bulk Δp was imposed by valinomycin-induced K⁻ diffusion potentials of different size while the initial ΔG_fp was varied. In all cases equilibrium was reached in about 1.5 h. A high H⁻/ATP ratio was also deduced from the relation between the initial rates of ATP synthesis or hydrolysis at varying ΔG_fp and Δp. The implications of these results for the mechanism of energy transduction in energy-conserving membranes are discussed.     

A calorimetric study of the binding of 2'-deoxyuridine-5'-phosphate and 5-fluoro-2'-deoxyuridine-5'-phosphate to thymidylate synthetase.

The thermodynamic parameters, ΔH′, ΔG′, and ΔS′, and the stoichiometry for the binding of the substrate 2′-deoxyuridine-5′-phosphate (dUMP) and the inhibitor 5-fluoro-2′-deoxyuridine-5′-phosphate (FdUMP) to Lactobacillus casei thymidylate synthetase (TSase) have been investigated using both direct calorimetric methods and gel filtration methods. The data obtained show that two ligand binding sites are available but that the binding of the second mole of dUMP is extremely weak. Binding of the first mole of dUMP can best be illustrated by dUMP + TSase + H⁺?(dUMP-TSase-H⁺). [1] The enthalpy, ΔH₁′, for reaction [1] was measured directly on a flow modification of a Beckman Model 190B microcalorimeter. Experiments in two different buffers (I = 0.10 m) show that ΔH₁′ = ?28 kJ mol^?1 and that 0.87 mol of protons enters into the reaction. Analysis of thermal titrations for reaction [1] indicates a free energy change of ΔG₁′ = ?30 kJ mol^?1 (K₁ = 1.7 × 10⁵ m^?1). From these parameters, ΔS₁′ was calculated to be +5 J mol^?1 degree^?1, showing that the reaction is almost totally driven by enthalpy changes. Gel filtration experiments show that at very high substrate concentrations, binding to a second site can be observed. Gel filtration experiments performed at low ionic strength (I = 0.05 m) reveal a stronger binding, with ΔG₁′ = ?35 kJ mol^?1 (K₁ = 1.2 × 10⁶ m^?1), suggesting that the forces driving the interaction are, in part, electrostatic. Addition of 2-mercaptoethanol (0.10 m) had the effect of slightly increasing the dUMP binding constant. Binding of FdUMP to TSase is best illustrated by 2FdUMP + TSase + n_HH⁺?FdUMP₂ ? TSase ? (H⁺)_nH. [2] The enthalpy for this reaction, ΔH₂, was also measured calorimetrically and found to be ?30 kJ mol^?1 with n_H = 1.24 at pH 7.4 Assuming two FdUMP binding sites per dimer as established by Galivan et al. [Biochemistry15, 356–362 (1976)] our calorimetric results indicate different binding energies for each site. Based on the binding data, a thermodynamic model is presented which serves to rationalize much of the confusing physical and chemical data characterizing thymidylate synthetase.     

The phosphorylation potentials generated by respiring Ehrlich ascites tumor mitochondria

The extra- and intramitochondrial phosphorylation potentials (ΔG_p(out) and ΔG_p(in), respectively) generated by respiring Ehrlich ascites tumor mitochondria were determined, using succinate, pyruvate + malate, ascorbate + N,N,N′,N′-tetramethyl-p-phenylenediamine, and ascorbate + ferrocyanide as substrate systems. Values of ΔG_p(out) exceeding 15 kcal mol^?1 (62.8 kJ mol^?1) in post-ADP state 4 respiration were found with succinate as substrate, in agreement with data on normal rat liver mitochondria. ΔG_p(out) values exceeding 15 kcal mol^?1 (62.8 kJ mol^?1) were also observed with ascorbate + TMPD or ascorbate + ferrocyanide as substrates. Slightly lower values of ΔG_p(out) were found with the NAD-linked substrates pyruvate + malate. The intramitochondrial ΔG_p(in) developed by respiring Ehrlich ascites tumor mitochondria respiring on succinate approached 12 kcal mol^?1 (50.2 kJ mol^?1), in agreement with reported values on rat liver mitochondria. The prior accumulation of Ca²⁺ and phosphate by the Ehrlich cell mitochondria did not lower the extramitochondrial ΔG_p(out) developed after a subsequent addition of ADP. Although the rate of oxidative phosphorylation of Ehrlich ascites tumor cells is reduced by intramitochondrial Ca²⁺ and phosphate (Villalobo and Lehninger (1980) J. Biol. Chem., 255, 2457–2464) they are still capable of generating ATP in the suspending medium against a high thermodynamic gradient, as expressed by the [ATP]/[ADP][P_i]mass action ratio.     

Kinetic and Energetic Model for the Primary Processes in Photosystem II

A detailed model for the kinetics and energetics of the exciton trapping, charge separation, charge recombination, and charge stabilization processes in photosystem (PS) II is presented. The rate constants describing these processes in open and closed reaction centers (RC) are calculated on the basis of picosecond data (Schatz, G. H., H. Brock, and A. R. Holzwarth. 1987. Proc. Natl. Acad. Sci. USA. 84:8414-8418) obtained for oxygen-evolving PS II particles from Synechococcus sp. with ~80 chlorophylls/P₆₈₀. The analysis gives the following results. (a) The PS II reaction center donor chlorophyll P₆₈₀ constitutes a shallow trap, and charge separation is overall trap limited. (b) The rate constant of charge separation drops by a factor of ~6 when going from open (Q-oxidized) to closed (Q-reduced) reaction centers. Thus the redox state of Q controls the yield of radical pair formation and the exciton lifetime in the Chl antenna. (c) The intrinsic rate constant of charge separation in open PS II reaction centers is calculated to be ~2.7 ps^-1. (d) In particles with open RC the charge separation step is exergonic with a decrease in standard free energy of ~38 meV. (e) In particles with closed RC the radical pair formation is endergonic by ~12 meV. We conclude on the basis of these results that the long-lived (nanoseconds) fluorescence generally observed with closed PS II reaction centers is prompt fluorescence and that the amount of primary radical pair formation is decreased significantly upon closing of the RC.     

Revisiting the Association of Cationic Groove-Binding Drugs to DNA Using a Poisson-Boltzmann Approach

Proper modeling of nonspecific salt-mediated electrostatic interactions is essential to understanding the binding of charged ligands to nucleic acids. Because the linear Poisson-Boltzmann equation (PBE) and the more approximate generalized Born approach are applied routinely to nucleic acids and their interactions with charged ligands, the reliability of these methods is examined vis-à-vis an efficient nonlinear PBE method. For moderate salt concentrations, the negative derivative, SK_pred, of the electrostatic binding free energy, ΔG_el, with respect to the logarithm of the 1:1 salt concentration, [M⁺], for 33 cationic minor groove drugs binding to AT-rich DNA sequences is shown to be consistently negative and virtually constant over the salt range considered (0.1-0.4 M NaCl). The magnitude of SK_pred is approximately equal to the charge on the drug, as predicted by counterion condensation theory (CCT) and observed in thermodynamic binding studies. The linear PBE is shown to overestimate the magnitude of SK_pred, whereas the nonlinear PBE closely matches the experimental results. The PBE predictions of SK_pred were not correlated with ΔG_el in the presence of a dielectric discontinuity, as would be expected from the CCT. Because this correlation does not hold, parameterizing the PBE predictions of ΔG_el against the reported experimental data is not possible. Moreover, the common practice of extracting the electrostatic and nonelectrostatic contributions to the binding of charged ligands to biopolyelectrolytes based on the simple relation between experimental SK values and the electrostatic binding free energy that is based on CCT is called into question by the results presented here. Although the rigid-docking nonlinear PB calculations provide reliable predictions of SK_pred, at least for the charged ligand-nucleic acid complexes studied here, accurate estimates of ΔG_el will require further development in theoretical and experimental approaches.     

Stereodynamics of tetramezine

The antidepressant drug tetramezine [1,2‐bis‐(3,3‐dimethyldiaziridin‐1‐yl)ethane] consists of two bridged diaziridine moieties with four stereogenic nitrogen centers, which are stereolabile and, therefore, are prone to interconversion. The adjacent substituents at the nitrogen atoms of the diaziridines moieties exist only in an antiperiplanar conformation, which results in a coupled interconversion. Therefore, three stereoisomers exist (meso form and two enantiomeric forms), which epimerize when the diaziridine moieties are regarded as stereogenic units due to the coupled interconversion. Here, we have investigated the epimerization between the meso and enantiomeric forms by dynamic gas chromatography. Temperature‐dependent measurements were performed, and reaction rate constants were determined using the unified equation of chromatography implemented in the software DCXplorer. The activation barriers of the epimerization were found to be ΔG^≠ = 100.7 kJ mol^?1 at 25°C and ΔG^≠ = 104.5 kJ mol^?1 at 37°C, respectively. The activation enthalpy and entropy were determined to be ΔH^≠ = 70.3 ± 0.4 kJ mol^?1 and ΔS^≠ = ?102 ± 2 J mol^?1 K^?1. Chirality, 2011. © 2010 Wiley‐Liss, Inc.