Technical Comments

Response to Comment on “The Silicate-Mediated Formose Reaction: Bottom-Up Synthesis of Sugar Silicates”

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Science  20 Aug 2010:
Vol. 329, Issue 5994, pp. 902
DOI: 10.1126/science.1188978

Abstract

We reported that silicate mediates the formation of four-carbon and six-carbon sugars from simple two- and three-carbon molecules. Kim and Benner’s contention that silicate has little impact on these reactions is based on experiments using harsher conditions of temperature, pH, silicate concentration, and reaction time than in our study, thus confounding any comparisons between our results.

We reported that two- and three-carbon molecules (glycoaldehyde and glyceraldehyde), in the presence of aqueous sodium silicate, spontaneously form silicate complexes of four-carbon and six-carbon sugars, respectively (1). In their comment, Kim and Benner (2) present new, unpublished experiments concerned with the mediation of carbohydrate synthesis by silicate salts in aqueous solution. Their experiments were carried out under very different conditions from those reported by us, and with very different objectives.

We detailed the conditions of our reactions in the supporting online material (SOM) accompanying our report (1) and specified them in our cited work (3). The unbuffered pH of the starting sodium silicate solution used in our experiments was 11.7. The organic starting materials are acidic, producing aqueous solutions of pH ~4.0. Consequently, on addition of the substrates to sodium silicate, the unbuffered pH shifts to the range 9 to 11, depending on the starting material, its concentration, and the concentration of sodium silicate. Thus, the pH of our silicate reactions was less basic than those of Kim and Benner (buffered 11.8), and our solutions contained almost 500 times less base (0.45 versus 220 mM). Their statement that they appear to have used the same concentrations of silicate that we did is incorrect. It is unlikely that prebiotic conditions would be buffered, so we felt that unbuffered conditions were more realistic. Our NaOH solutions as prepared have a pH of about 13; upon addition of the substrates, the pH drops to ~12. Kim and Benner carried out reactions for 1 hour at 65°C and for 4 days at room temperature. These conditions are considerably harsher than ours, as our reactions were complete after <30 min at room temperature. Thus, Kim and Benner (2) used longer times, higher temperatures, higher pH, and higher silicate concentration. These conditions are likely to create very different results from those reported by us.

The majority of our report (1) was concerned with the effect of silicate on the separate oligomerizations of glycoaldehyde (C2) and of glyceraldehyde (C3). Kim and Benner’s comments are concerned only with the cross-reaction of C2 with C3; they do not discuss their independent dimerizations. We included the cross-reaction of C2 and C3 peripherally, with data primarily in the SOM for (1). The primary result of our study was the clean conversion of C3 to C6 sugars as mediated by silicates. Although we did not specifically mention arabinose as a product of C2+C3, we are in complete agreement that, as the thermodynamic C5 product, it would likely be major under the conditions used by Kim and Benner. Their statement that a role for silicate in guiding arabinose formation is incompatible with their results and their experiments on the stability of ribose at 65°C find no counterpart in our work, which did show that silicate stabilizes pentose formation from the reaction of C2 and C3 at room temperature.

In a 2004 study (4), Benner and colleagues published conditions involving borate that favor ribose production. A primary aim of Kim and Benner (2) now appears to be to demonstrate the greater effectiveness of borate than of silicate in this reaction. None of our experiments used borate or addressed this issue, except to note their difference in natural availability.

Kim and Benner state that our figure 2 in (1) “suggests that the ions being observed are different in the mixtures being compared.” This was our expressed intention. The reaction with NaOH produces free sugars directly; the reaction in the presence of sodium silicate produces silicate complexes. Figures 2 and 3 in (1) illustrated our approach. The lower pairs of spectra demonstrate that the free sugar products of either C2 or C3 quickly degrade in the presence of NaOH alone. The upper pairs of spectra demonstrate that the products in the presence of silicate degrade minimally or not at all. We also hydrolyzed the silicate products to the free sugars [figure S4 in (1)], so that comparisons could be made of free sugars with free sugars, with identical conclusions. We include new SOM herein of the 13C spectra for the silicate-mediated C2+C3 reaction at room temperature, of particular interest to Kim and Benner, showing the nearly unchanged nature of the products between 30 min and 24 hours (figs. S1 and S2). In the absence of silicate for the same reaction, the products rapidly degrade (figs. S3 and S4).

Kim and Benner disagree with our conclusion that silicate mediates formose-like aldol reactions, yet they did not examine the principal reactions we reported, of C2 or C3 alone. Figures 2, 3, S9, and S10 in (1) and figs. S1 to S4 presented here demonstrate dramatic differences between the oligomerization reaction in the presence and in the absence of silicate, as prima facie evidence of such mediation. In the most favorable case, hexose products from C3 remain nearly exclusive and unchanged between 30 min and 12 hours in the presence of silicate, whereas in its absence the same products degrade rapidly during this time period. Similar results occur with C2 alone, and with C2 and C3 together. The 13C spectra in figs. S1 to S4 demonstrate a strong mediating effect of silicate in the reaction of C2+C3 that mirrors the mass spectral results in our study [figure S10 in (1)]. Silicate clearly stabilizes C4 to C6 oligomers.

The second mediating role of silicate is more subtle. As demonstrated previously (3, 5, 6), only certain sugars can complex silicate, namely those with at least four carbons and possessing adjacent cis hydroxy groups in the furanose form. Only these oligomers survive as silicate complexes in the reaction mixtures [as shown in figures 2 and 3 in (1)]. We found no evidence for free sugars in these reaction mixtures before hydrolysis. We hypothesize that oligomers with the incorrect stereochemistry are in equilibrium with the smaller starting materials, which re-oligomerize. Eventually, silicate sequesters all products. In this manner, there is a strong selection for certain higher sugar stereochemistries.

It is likely that different results occur under Kim and Benner’s harsher conditions of temperature, pH, silicate concentration, and reaction time. Our study was not intended to address the relative prebiotic efficacies of borate and silicate or of arabinose selection. Rather, we demonstrated that under the conditions we reported, silicate exhibits the strong mediating effects of selecting stereochemistries on formation, sequestering the favored sugars as silicate complexes, and stabilizing them against decomposition.

Supporting Online Material

www.sciencemag.org/cgi/content/full/329/5994/902-b/DC1

Figs. S1 to S4

References

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