Energy Relationship Analysis Research Articles

5-Nitrosalicylaldehyde in aqueous co-solvent mixtures of methanol, ethanol, isopropanol and acetonitrile: Solubility determination, solvent effect and preferential solvation analysis

The equilibrium 5-nitrosalicylaldehyde solubility in methanol (1) + water (2), ethanol (1) + water (2), isopropanol (1) + water (2) and acetonitrile (1) + water (2) mixtures was determined by a shake-flask method from 273.15 K to 313.15 K under local pressure of 101.2 kPa. At the same mass fraction of methanol (ethanol, isopropanol or acetonitrile) and temperature, the mole fraction solubility of 5-nitrosalicylaldehyde was greater in (acetonitrile + water) mixture than in ethanol (1) + water (2), isopropanol (1) + water (2) and methanol (1) + water (2) mixtures. The relative importance of solute–solvent and solvent–solvent interactions upon the solubility variation was valued by using the linear solvation energy relationship analysis of solvent effect. The method of inverse Kirkwood–Buff integrals was used to study the preferential solvation on the basis of thermodynamic solution properties. The preferential solvation parameters for methanol, ethanol, isopropanol and acetonitrile were positive in the four mixtures in co-solvent-rich and intermediate composition, indicating that 5-nitrosalicylaldehyde was solvated preferentially by the co-solvent. It is conjecturable that in these regions 5-nitrosalicylaldehyde acts as a Lewis acid with the alcohols’ molecules; while for the acetonitrile + water mixture, the preferential solvation could be attributed to polarization effects. Moreover, the drugs’ solubility was mathematically represented via the Jouyban-Acree model acquiring the average relative deviations<6.03%.

Analysis of the aqueous solubility of trialkyl phosphates, dialkyl alkylphosphonates, dialkylphosphites and alkyl dialkylphosphinates

Linear free energy relationship (LFER) analysis based on the molar intrinsic volume (Vx), McGowan hydrophile‒lipophile balance (HLB) and cumulative Kabachnik constants (Σσϕ) of considered solutes has been performed for the solubility of trialkyl phosphates, dialkyl alkylphosphonates, dialkyl phosphites and alkyl dialkylphosphonates in pure water (called also as their aqueous solubility). The descriptors mentioned above are known for all considered solutes and are strongly correlated with their aqueous solubility. From the correlation found for trialkyl phosphates, dialkyl alkylphosphonates and dialkyl phosphites it follows that the mean contribution of each methylene group in their structure (Δlog Sw) is a constant for these homologous series and equal to − 0.41. It means that within of homologous series the aqueous solubility of succeeding solutes decreases regularly. The established increment has been further used as a tool for the preliminary selection of solutes whose aqueous solubility at 25 °C is in agreement with this condition. The adequate model (further denoted as AR model) based on the accessible data of temperature effects upon the aqueous solubility of tributyl phosphate, dibutyl butylphosphonate and butyl dibutylphosphinate has been formulated and then tested with positive results for the other solutes whose solubility is known at a selected constant temperature, e.g. at 25 °C. It should noticed, however, that in this case there are some serious restrictions. First, the interpretation and formulation of conclusions for the solutes which aqueous solubility is known at one selected temperature (e.g. 25 °C) or if it has been determined at a few temperatures only, should be made with care. Second, the obtained results with AR model cannot be used for prediction of temperature effects upon the aqueous solubility of such solutes. Simultaneously, the results obtained with AR model have been compared with those following from the modified Abraham model. Such comparison has been possible due to a significant progress in the different application of Abraham model for several organophosphorus derivatives as monobasic dialkyl- and diarylphosphoric acids, dialkyl- and diphenylphosphinic acids, trialkyl- and triaryl phosphates, dimethyl methylphosphonate, dialkylphosphites and some of trialkyl- and triarylphosphine oxides, respectively.

Thermodynamic solubility modelling, solvent effect and preferential solvation of p-nitrobenzamide in aqueous co-solvent mixtures of dimethyl sulfoxide, ethanol, isopropanol and ethylene glycol

The equilibrium p-nitrobenzamide solubility in mixtures of dimethyl sulfoxide (DMSO, 1) + water (2), ethanol (1) + water (2), isopropanol (1) + water (2) and ethylene glycol (EG, 1) + water (2) was determined with a shake-flask method from (293.15 to 328.15) K under atmospheric pressure (101.1 kPa). At the same temperature and mass fraction of DMSO (ethanol, isopropanol or EG), the mole fraction solubility of p-nitrobenzamide was greater in (DMSO + water) than in ethanol (1) + water (2), isopropanol (1) + water (2) and ethylene glycol (EG, 1) + water (2) mixtures. X-Ray power diffraction analysis of solid phase showed no polymorphic transformation or solvate formation in experiments. The degree of relative importance of solute–solvent and solvent–solvent interactions on the solubility variation was evaluated by the linear solvation energy relationship analysis of solvent effect. The inverse Kirkwood–Buff integrals was used to study the preferential solvation based on thermodynamic solution properties. The parameters of preferential solvation for ethanol and isopropanol were positive in the ethanol (1) + water (2) and isopropanol (1) + water (2) mixtures in co-solvent-rich and intermediate composition, indicating that p-nitrobenzamide was solvated preferentially by the co-solvent. p-Nitrobenzamide acted mainly as a Lewis acid interacting with proton-acceptor functional groups of the co-solvents. Moreover, the drugs’ solubility was represented mathematically via the Jouyban-Acree model attaining the average relative deviations smaller than 2.16%.

Atroposelective Catalytic Asymmetric Allylic Alkylation Reaction for Axially Chiral Anilides with Achiral Morita-Baylis-Hillman Carbonates.

A highly efficient method to access axially chiral anilides through asymmetric allylic alkylation reaction with achiral Morita-Baylis-Hillman carbonates by using a biscinchona alkaloid catalyst was reported. Through the atroposelective approach, a broad range of axially chiral anilide products with different acyl groups, such as substituted phenyl, naphthyl, alkyl, enyl, styryl, and benzyl, were generated with very good yields, moderate to excellent cis: trans ratios, and good to excellent enantioselectivities. The reaction can be scaled up, and the synthetic utility of axially chiral anilides was proved by transformations. Moreover, the linear free energy relationship analysis was introduced to investigate the reaction.

Separation of binary mixtures based on gamma infinity data using [OMMIM][BF4] ionic liquid and modelling of thermodynamic functions

The activity coefficients at infinite dilution (γi∞), gas-liquid partition coefficients (KL) of organic solutes (n-alkanes, alkenes, alkyl benzenes, acetonitrile, acetone, tetrahydrofuran, ethyl acetate, 1,4-dioxane, chloromethanes, alcohols and cycloalkene) in the ionic liquid 1-octyl-2,3-dimethylimidazolium tetrafluoroborate ([OMMIM][BF4]) have been measured using the gas-liquid chromatographic method (GLC) at five temperatures (313.15 K–353.15 K). The density of [OMMIM][BF4], as a function of temperature, was determined in atmosphere pressure p = 101.3 kPa. The values of the partial molar excess enthalpies at infinite dilution (H-iE,∞) were derived from the temperature dependence of the lnγi∞ values at a reference temperatureTref = 298.15 K. The entropies (TrefS-iE,∞) and Gibbs free energies (G-iE,∞) of organic solutes in [OMMIM][BF4] at a reference temperatureTref = 298.15 K were calculated from the γi∞ values. The Hildebrand’s solubility parameters of [OMMIM][BF4] were determined by the regular solution theory (RST) combined with Flory ‘‘combinatorial’’ equation. The interaction between the IL and the individual solutes can be disclosed and the nature of force for IL was explored by the linear free energy relationship (LFER) analysis. Selectivity (Sij∞) and capacity (kj∞) at infinite dilution at 323.15 K have been determined for n-hexane (i)/benzene (j), cyclohexane (i)/benzene (j). The results were analysed in comparison to literature data for alkylimidazolium ionic liquids (ILs) with [BF4]-.

Experimental solubility evaluation and thermodynamic analysis of biologically active D-tryptophan in aqueous mixtures of N,N-dimethylformamide and several alcohols

The D-tryptophan solubility in aqueous solutions of methanol, ethanol, isopropanol and N,N-dimethylformamide (DMF) was measured by the saturation shake-flask method at temperatures ranging from 283.15 K to 333.15 K. The maximum solubility was found in water for alcohol (1) + water (2) mixtures, and in neat DMF for DMF (1) + water (2) mixture. When the same temperature and mass fraction of the water is given, the highest mole fraction solubility of D-tryptophan was found in (DMF + water). The solid phases were tested by X-ray powder diffraction (XPRD) showing no polymorphic transformation, solvate formation or crystaltransition. Three solubility models, i.e. the Jouyban-Acree, van’t Hoff-Jouyban-Acree and Apelblat-Jouyban-Acree were employed to correlate the experimental solubility values so as to obtain thermodynamic parameters. The RAD and RMSD data were no more than 1.65% and 9.40 × 10−5, respectively. Linear solvation energy relationship analysis based on Kamlet-Taft parameters indicated that the variation of D-tryptophan solubility depended on π∗ for methanol (ethanol, isopropanol) (1) + water (2), and cavity term for DMF (1) + water (2). The preferential solvation parameters (δx1,3) for methanol, ethanol, isopropanol and DMF derived by means of the inverse Kirkwood–Buff integrals were negative in the four solvent mixtures with intermediate and alcohol-rich compositions, which indicated that D-tryptophan was preferentially solvated by water. The higher solvation by water could be explained in terms of the higher acidic behaviour of the solvents interacting with the Lewis basic groups of the D-tryptophan. However D-tryptophan is preferentially solvated neither by water nor by DMF in DMF + water mixture.

Linear free energy relationship analysis of permeability across polydimethylsiloxane (PDMS) membranes and comparison with human skin permeation in vitro

The aim of the present work is to evaluate the similarity between PDMS membranes and human skin in vitro in permeation study by linear free energy relationship (LFER) analyses. The values of the permeability coefficient log Kp (cm/s) under reliable experimental conditions were collected from the literature for a set of 94 compounds including both neutral and ionic species, which cover a broad range of structural diversity. The values of log Kp (cm/s) have been correlated with Abraham descriptors to yield an equation with R2 = 0.952 and SD = 0.38 log units. The established LFER model for log Kp (cm/s) across PDMS membranes showed no close analogy with that through human skin in vitro. A further critical analysis of the coefficients of the LFER models confirmed that the PDMS permeation system is a very poor model for human skin permeation.

Thermodynamics and selectivity of separation based on activity coefficients at infinite dilution of various solutes in ionic liquid [HMMIM][BF4

Abstract The activity coefficients at infinite dilution ( γ i ∞ ), gas–liquid partition coefficients ( K L ) of organic solutes (n-alkanes, alkenes, alkyl benzenes, acetonitrile, acetone, tetrahydrofuran, ethyl acetate, chloromethanes, alcohols and 1,4-dioxane) in the ionic liquid 1-Hexyl-2,3-dimethylimidazolium tetrafluoroborate ([HMMIM][BF4]) have been measured using the gas–liquid chromatographic method (GLC) at five temperatures: 313.15 K, 323.15 K, 333.15 K, 343.15 K, 353.15 K. The density of [HMMIM][BF4], as a function of temperature, was determined in atmosphere. The values of the partial molar excess enthalpies at infinite dilution ( H ‾ i E , ∞ ) were derived from the temperature dependence of the In γ i ∞ values. The entropies ( T ref S ‾ i E , ∞ ) and Gibbs energies ( G ‾ i E , ∞ ) of organic solutes in [HMMIM][BF4] at a reference temperature T r ef = 298.15 K were calculated from the γ i ∞ values. The Hildebrand’s solubility parameters of the IL [HMMIM][BF4] were determined by the regular solution theory (RST) combined with Flory ‘‘combinatorial’’ equation. Selectivity ( S ij ∞ ) and capacity ( k j ∞ ) at infinite dilution at 323.15 K have been determined for n-hexane ( i )/benzene (j), cyclohexane ( i )/benzene (j). The results were analyzed in comparison to literature data for alkylimidazolium ionic liquids (ILs) with [ BF 4 ] - . The interaction between the IL and the individual solutes can be disclosed by the linear free energy relationship (LFER) analysis.

The Properties of the Nucleodur HILIC Stationary Phase in Supercritical Fluid Chromatography

The Nucleodur HILIC zwitterionic stationary phase was characterized by linear solvation energy relationship (LSER) analysis in the supercritical fluid chromatography mode. It was shown that the main contribution to retention is made by hydrogen bonding interactions.

Separation of binary mixtures based on gamma infinity data using [OMMIM][NTf 2 ] ionic liquid and modelling of thermodynamic functions

Abstract Activity coefficients at infinite dilution ( γ i ∞ ) and (gas-liquid) partition coefficients ( K L ) for organic compounds (alkanes, alkenes, alkyl benzenes, acetonitrile, acetone, tetrahydrofuran, ethyl acetate, 1,4-dioxane, chloromethanes, and alcohols) in the ionic liquid (IL) 1-octyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide ([OMMIM][NTf2]) have been measured by the gas-liquid chromatographic(GLC) method in the temperature range of (313.15 to 353.15) K. Density, ρ as a function of temperature for [OMMIM][NTf2] at pressure p = 101.3 kPa were measured. The values of the partial molar excess enthalpies at infinite dilution ( H ¯ i E , ∞ ) were derived from the temperature dependence of the γ i ∞ values. The entropies ( T r ef S ¯ i E , ∞ ) and Gibbs energies ( G ¯ i E , ∞ ) of organic solutes in [OMMIM][NTf2] at a reference temperature T r ef = 298.15 K were also calculated from the γ i ∞ values. The Hildebrand’s solubility parameters of the IL [OMMIM][NTf2] were also determined by the regular solution theory (RST) combined with Flory “combinatorial” equation. The linear free energy relationship (LFER) analysis of the results was performed to disclose molecular interactions operating between the IL and the individual solutes. Selectivity ( S i j ∞ ) and capacity ( k j ∞ ) at infinite dilution at 323.15 K have been determined for n-hexane ( i )/benzene ( j ), cyclohexane ( i )/benzene ( j ) and compared to literature values for [NTf2]-based ILs for the same separation problems. For three isomeric xylenes separation problems, S i j ∞ at 323.15 K was also obtained from the γ i ∞ values.

Determination of lipid bilayer affinities and solvation characteristics by electrokinetic chromatography using polymer-bound lipid bilayer nanodiscs.

Styrene-maleic acid polymer-bound lipid bilayer nanodiscs have been investigated and characterized by electrokinetic chromatography. Linear solvation energy relationship analysis was employed to characterize the changes in solvation environment of nanodiscs of varied belt to lipid ratio, belt polymer chemistry and molecular weight, and lipid composition. Increases in the lipid to belt polymer ratio resulted in smaller, more cohesive nanodiscs with greater electrophoretic mobility. Nanodisc structures with belt polymers of different chemistry and molecular weight were compared and showed only minor changes in solvent characteristics and selectivity consistent with changes in structure of the lipid bilayer. Seven phospholipid and sphingomyelin nanodiscs of different lipid composition were characterized. Changes in lipid head group structure had a significant effect on bilayer-solute interactions. In most cases, changes in alkyl tail structure had no discernible effect on solvation environment aside from those explained by changes in the gel-liquid transition temperature. Comparison to vesicles of similar lipid composition show only minor differences in solvation environment, likely due to differences in lipid composition and bilayer curvature. Together these results provide evidence that the dominant solute-nanodisc interactions are with the lipid bilayer and that head group chemistry has a greater impact on bilayer-solute interactions than alkyl tail or belt polymer structure. Nanodisc electrokinetic chromatography is demonstrated to allow characterization of solute interactions with lipid bilayers of varied composition.

Structural properties governing drug-plasma protein binding determined by high-performance liquid chromatography method

The high-performance liquid chromatography (HPLC) method employing stationary phases immobilized with plasma proteins was used for this study to investigate the structural properties governing drug-plasma protein binding. A set of 65 compounds with a broad range of structural diversity (in terms of volume, hydrogen-bonding, polarity and electrostatic force) were selected for this purpose. The Abraham linear free energy relationship (LFER) analyses of the retention factors on the immobilized HSA (human serum albumin) and AGP (α1-acid glycoprotein) stationary phases showed that McGowan’s characteristic molecular volume (V), dipolarity/polarizability (S) and hydrogen bond basicity (B) are the three significant molecular descriptors of solutes determining the interaction with immobilized plasma proteins, whereas excess molar refraction (E) is less important and hydrogen bond acidity (A) is not of statistical significance in both systems, for electrically neutral compounds. It was shown that ionised acids, as carboxylate anions, bind very strongly to the immobilized HSA stationary phase and that ionised bases, as cations bind strongly to the AGP stationary phase. This is the first time that the effect of ionised species on plasma protein binding has been determined quantitatively; the increased binding of acids to HSA is due almost entirely to acids in their ionised form.

Study on the Catalytic Behavior of Bifunctional Hydrogen-Bonding Catalysts Guided by Free Energy Relationship Analysis of Steric Parameters.

Free energy relationship (FER) studies to correlate steric parameters with the enantiocatalytic performance of bifunctional tertiary-amine hydrogen-bonding catalysts, including (S,S)-cyclohexane-1,2-diamine-derived thioureas, Cinchona alkaloid derived thioureas, and (S,S)-cyclohexane-1,2-diamine-derived squaramides, in Michael reactions revealed that the reactions are much favored by catalysts with less bulky N-substituents. The observed FERs are independent of the chiral scaffold and hydrogen-bond donor, and deepen the understanding of current bifunctional hydrogen-bonding catalysts. Moreover, DFT calculations were performed to interpret the observed high reactivities of thioureas with less bulky substituents. In particular, the computations demonstrated the advantage of a benzyl thiourea catalyst, in which an extra CH⋅⋅⋅π interaction between catalyst and substrate is the key factor.

Linear Free Energy Relationship Analysis of Transition State Mimicry by 3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) Oxime, a DAHP Synthase Inhibitor and Phosphate Mimic

3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthase catalyzes an aldol-like reaction of phosphoenolpyruvate (PEP) with erythrose 4-phosphate (E4P) to form DAHP in the first step of the shikimate biosynthetic pathway. DAHP oxime, in which an oxime replaces the ketone, is a potent inhibitor, with Ki = 1.5 μM. Linear free energy relationship (LFER) analysis of DAHP oxime inhibition using DAHP synthase mutants revealed an excellent correlation between transition state stabilization and inhibition. The equations of LFER analysis were rederived to formalize the possibility of proportional, rather than equal, changes in the free energies of transition state stabilization and inhibitor binding, in accord with the fact that the majority of LFER analyses in the literature demonstrate nonunity slopes. A slope of unity, m = 1, indicates that catalysis and inhibitor binding are equally sensitive to perturbations such as mutations or modified inhibitor/substrate structures. Slopes <1 or >1 indicate that inhibitor binding is less sensitive or more sensitive, respectively, to perturbations than is catalysis. LFER analysis using the tetramolecular specificity constant, that is, plotting log(KM,MnKM,PEPKM,E4P/kcat) versus log(Ki), revealed a slope, m, of 0.34, with r2 = 0.93. This provides evidence that DAHP oxime is mimicking the first irreversible transition state of the DAHP synthase reaction, presumably phosphate departure from the tetrahedral intermediate. This is evidence that the oxime group can act as a functional, as well as structural, mimic of phosphate groups.

Performance and selectivity of cationic nanoparticle pseudo‐stationary phases in electrokinetic chromatography

Electrokinetic chromatography (EKC) is a powerful analytical technique that uses an ionic pseudo-stationary phase (PSP) to separate neutral compounds. Although anionic surfactants are the most common choice for PSP, cationic latex nanoparticles are an attractive alternative. Reversible addition-fragmentation chain transfer (RAFT) polymerization was used to synthesize several types of diblock copolymers that self-assemble into latex nanoparticles, which were characterized by a variety of techniques including diffusion NMR. The performance of each nanoparticle as a PSP was studied by using a homologous series of ketones and linear solvation energy relationships (LSER) analysis. A cationic homopolymer coating was found to be necessary to prevent band broadening caused by analyte interactions with nanoparticles adsorbed to the capillary surface. No significant difference in methylene selectivity or LSER parameters was observed between nanoparticles with different cationic shells, but differences were observed between nanoparticles with different hydrophobic cores. Cationic latex nanoparticles behaved more like anionic latex nanoparticles than like cationic surfactants, suggesting that selectivity is primarily driven by the hydrophobic portion of a PSP. Cationic latex nanoparticles in combination with a homopolymer cationic capillary coating are an excellent choice for EKC analyses where an anodic electroosmotic flow is required.

Phospholipid bilayer affinities and solvation characteristics by electrokinetic chromatography with a nanodisc pseudostationary phase.

Phospholipid bilayer nanodiscs composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and synthetic maleic acid-styrene copolymer belts have been introduced as a pseudostationary phase (PSP) in electrokinetic chromatography and demonstrated good performance. The nanodiscs provide a suitable migration range and high theoretical plate counts. Using this nanodisc pseudostationary phase, the affinity of the bilayer structure for probe solutes was determined and characterized. Good correlation is observed between retention factors and octanol water partition coefficients for particular categories of solutes, but the general correlation is weak primarily because the nanodiscs show stronger affinity than octanol for hydrogen bond donors. This suggests that a more appropriate application of this technology is to measure and characterize interactions between solutes and lipid bilayers directly. Linear solvation energy relationship analysis of the nanodisc-solute interactions in this study demonstrates that the nanodiscs provide a solvation environment with low cohesivity and weak hydrogen bond donating ability, and provide relatively strong hydrogen bond acceptor strength.

Kinetic Insights into the Binding between the nSH3 Domain of CrkII and Proline-Rich Motifs in cAbl

The interaction between CrkII and cAbl is implicated in diverse cellular processes. This interaction starts with the binding of the N-terminal Src homology 3 (nSH3) domain of CrkII to the proline-rich motifs of cAbl (PRMscAbl). Despite its critical importance, the detailed binding mechanism between the nSH3 domain and PRMs remains elusive. In this study, we used nuclear magnetic resonance Carr-Purcell-Meiboom-Gill relaxation dispersion experiment to study the binding kinetics between the nSH3 domain of CrkII and PRMscAbl. Our results highlight that the nSH3 domain binds to three PRMscAbl with very high on- and off-rate constants, indicating the transient nature of the binding. To further characterize the binding transition state, we conducted the Eyring and linear free energy relationship analyses using temperature-dependent kinetic data. These data indicate that the binding transition state of the nSH3 domain and PRM is accompanied by small activation enthalpy, owing to partial desolvation of the transition state. These results also highlight the similarity between the transition and free states, in terms of structure and energetics. Although the binding of the nSH3 domain and PRM displays the features consistent with a diffusion-limited process within our experimental conditions, further tests are necessary to determine if the binding is a true diffusion-limited process.

Additive Mediated Syn-Anti Conformational Tuning at Nucleation to Capture Elusive Polymorphs: Remarkable Role of Extended π-Stacking Interactions in Driving the Self-Assembly

Understanding the process of prenucleation clustering at supersaturating stage is of significant importance to envisage the polymorphism in crystalline materials. Preferential formation of a thermodynamically stable crystal form suggests energetically favored patterns of interactions which control molecular aggregation during nucleation. Introduction of additives during crystallization is sometimes used as a suitable strategy to obtain metastable polymorphs in cases where it is not easy to capture the same by conventional crystallization methods. Comparative analysis of energy relationships and intermolecular interactions between thermodynamically stable and metastable crystal forms provides valuable clues about the nature of growth synthons at prenucleation clustering and preferential crystallization of the thermodynamic form. Conformationally flexible sulfonamide/sulfoester derivatives constituting electron rich and electron-deficient aromatic rings were synthesized to study the interplay between π-stac...

Sequential Events during Capsaicin-Induced TRPV1 Activation

TRPV1 is a polymodal receptor for capsaicin, heat, and other noxious stimuli. Using an iterative approach combining computational docking and functional tests such as thermodynamic mutant cycle analysis, we recently identified two hydrogen bonds between the amide neck and vanillyl head of capsaicin and T551 (in S4) and E571 (in S4-S5 linker), respectively, of mouse TRPV1. Computational docking to various gating states and interpolated elastic network modeling (iENM) both suggested that the neck-T551 hydrogen bond forms first, followed by formation of the head-E571 hydrogen bond. To test this prediction and reveal the sequential events during capsaicin-induced TRPV1 activation, we carried out a rate-equilibrium linear free energy relationship (LFER) analysis. Residues of the capsaicin-activation machinery are perturbed with a series of point mutations. Single-channel recordings from these mutant channels yielded log-log plots of the opening rate constant versus the equilibrium constant. The slope of this plot, or the phi value, reflects the relative timing of movement by each residue during the closed-to-open transition, with a larger value indicating an earlier event. The phi analysis clearly revealed that the head-E571 hydrogen bond forms after the neck-T551 hydrogen bond. Applying this analysis to residues along the capsaicin-activation machinery will yield a temporal sequence of movements that may offer new insights into the structural mechanism underlying TRPV1 activation by capsaicin.

Kinetics versus thermodynamics in the proline catalyzed aldol reaction.

In this paper the equilibrium properties of the proline catalyzed aldol reaction was studied. The use of well-established methodologies, like reaction progress kinetic analysis and linear free energy relationship analysis, led to the quantification of the reaction reversibility and to its correlation with the substrate electronic activation. Due to these experimental observations, common computational approaches based on a one way transition state analysis become unsuitable. Therefore, a computational model based on the integration of a system of kinetic differential equations associated to the multiple equilibrium reactions was proposed. Such a model was found to successfully rationalize the chemical and stereochemical outcomes of this paradigmatic reaction for the first time.