On the Complexity of Kinetics and the Mechanism of the Thiosulfate–Periodate Reaction

Debugging periodate oxidation of cellulose: Why following the common protocol of quenching excess periodate with glycol is a bad idea

Periodate oxidation of cellulose to produce "dialdehyde cellulose" (DAC) has lately received increasing attention in sustainable materials development. Despite the longstanding research interest and numerous reported studies, there is still an enormous variation in the proposed preparation and work-up protocols. This apparently reduces comparability and causes reproducibility problems in DAC research. Two simple but prevalent work-up protocols, namely glycol quenching and filtration/washing, were critically examined and compared, resulting in this cautionary note. Various analytical techniques were applied to quantify residual iodine species and organic contaminations from quenching side reactions. The commonly practiced glycol addition cannot remove all oxidising iodine compounds. Both glycol and the formed formaldehyde are incorporated into DAC's polymeric structure. Quenching of excess periodate with glycol can thus clearly be discouraged. Instead, simple washing protocols are recommended which do not bear the risk of side reactions with organic contaminants. While simple washing was sufficient for mildly oxidised celluloses, higher oxidised samples were more likely to trap residual (per)iodate, as determined by thiosulfate titration. For work-up, simple washing with water is proposed while determining potential iodine contaminations after washing with a simple colorimetric test and, if needed, removal of residual periodate by washing with an aqueous sodium thiosulfate solution.

Systematic Application of the Principle of Detailed Balancing to Complex Homogeneous Chemical Reaction Mechanisms

It is not uncommon for proposed complex reaction mechanisms to violate the principle of detailed balancing. Here, we draw attention to three ways in which such violations can occur: reversible reaction loops where the rate constants do not attain closure, illegal loops, and reversible steps having rate equations in the forward and reverse directions that are inconsistent with the equilibrium expressions. We present two simple methods to test whether a proposed mechanism is consistent with the first two aspects of the principle of detailed balancing. Both methods are restricted to closed homogeneous isothermal reactions having mechanisms that consist of stoichiometrically balanced reaction steps. The first method is restricted to mechanisms in which all reaction steps are reversible; values of Δ_f G° are assigned to all reaction species, equilibrium constants are then computed for all steps, and all rate constants for elementary steps are constrained by the relationship K_eq = k_f/ k_r. The second method is applicable to mechanisms that can consist of a series of reversible and/or irreversible reaction steps. One first examines the subset of reversible steps to determine whether any of these steps are stoichiometrically equivalent to a combination of any of the other steps. If so, the forward and reverse rate expressions must yield equilibrium constants that are in agreement with the stoichiometric relationships. Next, the complete set of steps is examined to look for "illegal reaction loops". Both of these procedures are performed by constructing matrices that represent the stoichiometries of the various reaction steps and then performing row reductions to identify basis sets of loops. A method based on linear programming is described that determines whether a mechanism contains any illegal loops. These methods are applied in the analysis of several published reaction mechanisms.

Thermodynamic origin of α-helix stabilization by side-chain cross-links in a small protein

Peptide cross-linking has been widely explored as a means of constraining short sequences into stable folded conformations, most commonly α-helices. The prevailing hypothesis for the origin of helix stabilization is an entropic effect resulting from backbone pre-organization; however, obtaining direct evidence bearing on this hypothesis is challenging. Here, we compare the folding thermodynamics of a small helix-rich protein domain and analogues containing one of three common cross-linking motifs. Analysis of the folding free energy landscapes of linear vs. cyclized species reveal consistent trends in the effect of cyclization on folding energetics, as well as subtle differences based on the chemistry of the cross link. Stabilization in all three systems arises entirely from a reduction in the entropic penalty of folding that more than compensates for an enthalpic destabilization of the folded state.

Clarifying the Equilibrium Speciation of Periodate Ions in Aqueous Medium

Equilibria of periodate ion were reinvestigated in aqueous solution by using potentiometric titration, UV and Raman spectroscopies, and gravimetry simultaneously at 0.5 M ionic strength and at 25.0 ± 0.2 °C. Stepwise acid dissociation constants of orthoperiodic acid were found to be pK₁ = 0.98 ± 0.18, pK₂ = 7.42 ± 0.03, and pK₃ = 10.99 ± 0.02, as well as pK₂ = 7.55 ± 0.04 and pK₃ = 11.25 ± 0.03 in the presence of sodium nitrate and sodium perchlorate as background salts, respectively. pK₁ cannot be determined unambiguously from our experiments in the presence of sodium perchlorate. The molar absorptivity spectrum of H₄IO₆^- and H₃IO₆^2- was determined in the range of 215-335 nm, as major species of periodate present from slightly acidic to slightly alkaline conditions. The solubility of periodate decreases significantly under alkaline conditions, and it was determined to be (2.8 ± 0.4) mM by gravimetry, under our experimental conditions. None of these studies gave any clear evidence for an ortho-meta equilibrium and the frequently invoked dimerization of periodate. All measurements can quantitatively be described by the presence of orthoperiodic acid and its three successive deprotonation steps.

Oxime side-chain cross-links in an α-helical coiled-coil protein: structure, thermodynamics, and folding-templated synthesis of bicyclic species

Covalent side-chain cross-links are a versatile method to control peptide folding, particularly when α-helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein-protein complex. A series of sequence variants of the dimeric coiled coil GCN4-p1 bearing oxime bridges at solvent-exposed positions were prepared and biophysically characterized. Triggered unmasking of a side-chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X-ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an α-helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.