Here is Tour's article just referenced: inference-review.com
It's pretty long. Here are just a few excerpts:
.....
Making Molecules
Chemists study molecules. 1 Synthetic chemists make them. What nature does is anyone’s guess. The molecules that we make are made to perform certain functions. The initial design is important. Sometimes molecular designs are computer-assisted, but more often than not, the initial steps are done on paper. A target must first be drawn or otherwise designated. This is no trivial task. In some cases, chemists have seen the target in a related system; in other cases, they guess the target’s properties on the basis of its molecular weight, its shape, its addends, and its functional capacities.
This is just the beginning.
Once a target is selected, retrosynthesis is next, whether on paper or on a computer screen. Placing the target at the top, the chemist draws an inverted tree (or graph), one step down at a time, into multiple branch points, until he reaches a level where starting materials are at hand. 2
The decision tree is then pruned. Certain branches lead to dead ends. They are lopped off. Further refinement of various routes leads to a set of desired paths; these are the routes that can be attempted in the laboratory.
Why the retrosynthetic approach to complex molecules? It is because finding a direct path to a target is far too complicated. Dead ends are everywhere; dead products accumulate massively; and, between the dead ends and the dead products, precious starting materials tend to become exhausted.
There are no targets in evolution. Nature does not perform retrosynthetic analyses.
Given a target and a path to get there, the synthetic chemist must now try a number of chemical permutations. Each step may need to be optimized, and each step must be considered with respect to specific reaction site modifications and different reaction rates.
What is desired is often ever so slightly different in structure from what is not. If Product A is a mirror image of Product B, separation becomes a time-consuming and challenging task, one requiring complementary mirror-image structures. Many molecules in natural biological systems are homochiral. Their mirror images cannot do their work.
Few reactions ever afford a one hundred percent yield; few reactions are free of deleterious byproducts. Purification is essential. If byproducts are left in reaction, they result in complex mixtures that render further reactions impossible to execute correctly.
After purification, a number of different spectroscopic and spectrometric methods must be used to confirm the resulting molecular structures. Make the wrong molecular intermediate, the synthetic chemist quickly learns, and all subsequent steps are compromised.
Intermediate products are often unstable in air, sunlight or room light, or in water. Synthetic chemists work in seconds or minutes.
It is this laborious trench work that separates the men from the boys.
..................
Descent into DetailThe work that I have just described is merely an overview. The details are far richer. Consider the protocols for the conversion of compound 29 (Scheme 3) to nanocar 3b and their partial characterization data. 15
Protocol 1General Methods. All reactions were performed under an atmosphere of nitrogen unless stated otherwise. Reagent-grade diethyl ether and tetrahydrofuran (THF) were distilled from sodium benzophenone ketyl. Triethylamine (TEA) was distilled over CaH2. Fullerene (99.5+% pure) was purchased from MTR Ltd. And used as received. LHMDS (1M solution in THF) and TBAF (1M solution in THF) were obtained from Aldrich. Flash column chromatography was performed using 230–400 mesh silica gel from EM Science. Thin layer chromatography was performed using glass plates pre-coated with silica gel 40 F254 purchased from EM Science. Solution state 1H and 13C NMR spectra were recorded on 400 and 500 MHz spectrometers. Solid state NMR spectra were acquired at 200.13 MHz 1H, 50.33 MHz 13C, and 20.28 MHz 15N. Melting points were uncorrected. Ultra-sonicated fullerene slurry in THF was prepared in general ultrasonic cleaners.
General Procedure for the Addition of C60 to Terminal Alkynes Using LHMDS, in situ ethynylation method. To an oven-dried round bottom flask equipped with a magnetic stir bar was added the terminal alkyne and C60 (2 equiv per terminal alkyne H). After adding THF, the mixture was sonicated for at least 3 h. To the greenish-brown suspension formed after the sonication was added LHMDS dropwise at room temperature over 0.5 to 1.5h. As the reaction progressed, the mixture turned into a deep greenish-black solution. During the addition of the LHMDS, small aliquots from the reaction were extracted and quenched with TFA, dried, and re-dissolved in CS2 for TLC analysis (developed in a mixture of CS2, CH2Cl2 and hexanes). Completion of the reaction was confirmed by the disappearance of the starting materials. The reaction usually completed within 1.5 h from the beginning of LHMDS addition. Upon completion, the reaction was quenched with TFA to give a brownish slurry. Excess TFA and solvent were then removed in vacuo to afford a crude product that was purified by flash column chromatography (silica gel). Eluents and other slight modifications are described below for each compound.
Nanocar 3b. To a solution of compound 29 (Scheme 3), (0.096g, 0.030mmol) in THF (5mL) was added dropwise TBAF (0.2mL, 0.2mmol). 10 min after the addition of the TBAF, the reaction was quenched with saturated aqueous NH4Cl, and extracted twice with hexanes. The organic portion was dried over MgSO4 and filtered. After concentration in vacuo, the residue was purified by flash column chromatography with 30–42% CH2Cl2 in hexanes to give desilylated product (0.072g) as a yellow oil. This material was pure enough to carry on to the next reaction. The desilylated product (0.070g, 0.025mmol) was subjected to the general in situ ethynylation procedure with C60 (0.15g, 0.21mmol), THF (100mL), LHMDS (0.7mL, 0.7mmol), and TFA (0.7mL). (Note: product spot was not clearly visible on TLC analysis.) Crude products were dissolved in CS2 and directly loaded onto a column. The column was eluted with CS2/CH2Cl2 (100:1) to remove unreacted C60, and then with CS2/CH2Cl2 (1:1) for complete removal of trace C60 and elution of product. The product was further purified using another flash column with graduate elution of CS2/CH2Cl2/Hexanes (1:1:100), (3:2:5), then (3:3:4) to afford nanocar 3b (0.028g, 20%) as a brown solid. FTIR (CH2Cl2 cast) 2922, 2850, 2203, 1502, 1463, 1214cm-1; 1H NMR (500MHz, CDCl3) d 7.77 (d, J = 1.4 Hz, 2H), 7.58 (d, J = 8.0Hz, 2H), 7.51 (dd, J = 8.0Hz, 1.4Hz, 2H), 7.30 (s, 2H), 7.25 (s, 2H), 7.18 (s, 2H), 7.15 (s, 2H), 7.14 (s, 2H), 7.10 (s, 2H), 7.07 (s, 2H), 7.03 (s, 2H), 4.19–4.14 (m, 8H), 4.09 (m, 4H), 4.00 (m, 4H), 3.90–3.88 (m, 8H), 1.95–1.13 (m, 192H), 0.88–0.80 (m, 36H); 13C NMR (125MHz, CDCl3) d154.7, 154.6, 153.9, 153.75, 153.67, 153.65, (6 signals from aryloxy sp2-C in the aromatic ring), 151.65, 151.59, 151.497 (×2), 147.7 (×2), 147.44, 147.43, 146.74, 146.69, 146.50, 146.477 (×2), 146.46, 146.32 (×2), 146.31 (×2), 145.92, 145.89, 145.82, 145.77, 145.72, 145.69, 145.55, 145.529 (×2), 145.51, 145.45, 145.43, 144.78, 144.76, 144.60, 144.58, 143.28, 143.26, 142.69, 142.67, 142.66, 142.64, 142.21, 142.17, 142.13, 142.11, 142.07, 142.05, 141.98, 141.95, 141.77, 141.73, 141.69, 141.67, 140.47, 140.44, 140.40, 140.37, 136.18, 136.15, 135.3, 135.2, (30×2 signals from sp2-C in the C60 core), 134.4, 131.6, 130.9, 126.5, 125.8, 123.3, 117.6, 117.4 (×2), 117.2, 117.0, 116.9, 114.9, 114.7, 114.4, 114.2, 113.4, 113.2, 97.8, 96.1, 94.3, 94.1, 93.1, 92.2, 91.8, 91.0, 88.3, 80.2 (×2), 70.14, 70.10, 69.8, 69.6, 69.5, 69.3, 62.02, 61.98 (CH in the C60 core), 55.60, 55.59 (quaternary sp3-C in the C60 core), 32.04, 31.97, 31.95, 29.8, 29.74, 29.70, 29.66, 29.48, 29.45, 29.40, 22.77, 22.75, 22.73, 14.23, 14.21, 14.19; MALDI-TOF MS m/z (Sulfur as the matrix) calcd for C430H274O12 5632, found 5631 (M+).
These procedures are abbreviated and they are incomplete. 16 A skilled synthetic chemist will know what the abbreviations mean and how to complete the uncompleted steps. A simple statement such as, “All reactions were performed under an atmosphere of nitrogen unless otherwise stated,” means that most of those reactions would have failed if done in the open air. Pre-treatment of solvents was needed so that the system would not be contaminated by impurities, such as oxygen, which retard or mitigate the desired reactions. Purification was required at each step since the chemistry rarely affords the chemist materials that are of sufficient purity for use in subsequent steps.
Each product needed a different purification protocol.
Chance may favor the prepared mind, but good things rarely happen only by chance.
How does nature do it? Are the biologists sure that they know the answer?
Are they very sure?
..........................
In nature, molecular structure is confirmed by using complex molecules, the process akin to a glove fitting a hand. Whence that glove? It, too, had to be derived from a biological synthesis, with confirmation of its structure by a yet another glove that recognized its precise sequence, shape, and stereochemistry.
Designing nanoncars is child’s play in comparison to the complexity involved in the synthesis of proteins, enzymes, DNA, RNA, and polysaccharides, let alone their assembly into complex functional macroscopic systems. There are apparently a great many gloves in nature.
..................
Chemistry does not happen that way. Even the oxidative expulsion of SO2 from ketone 43 by the Ramberg–Bäcklund method would not work, since the sulfur is bound aromatically.
We could have left ketone 43 in a flask for millions of years and it would not form ketone 32 by any known or rational thermal, reductive, photochemical, or enzymatic method. This is not unusual when related compounds have clearly different starting points in organic chemistry. It is typical.
- That nature has a select set of molecules that can be transformed into related structures using very precise enzymes (catalysts) is a phenomenon unknown in any other field of organic chemistry.
..............
Most organic chemists would agree that even with extensive planning, 90% of reactions are failures. Substrates and conditions must be repeatedly modified to secure respectable and usable yields. At each step a massive amount of time is spent on separations and optimizations. If byproducts are permitted to accumulate, they can consume the new steps’ reagents and alter the course of the reaction. After every one or two steps there must be purification.
If all our reactions were near 100% yield, it would ease the separation problems. But this can take years to achieve, if it is possible at all. And even then, sufficient atom efficiency is very rare. Byproducts from the other reagents fill the system. High atom-efficient reactions are even harder to achieve. The loss of materials is expensive. In most cases, these byproducts cannot be converted back to usable compounds in an efficient way. Developing a scrubber system for degrading these products back to usable starting materials would, in most cases, take more time and money than developing the original target synthetic routes themselves. The separated byproducts are put into waste disposal containers and sent for destruction through combustion.
But we use petrochemicals as our major feedstocks, and these come in enormous amounts from fine-chemicals producers. Large amounts of energy come from power grids. - Don’t forget
We had the convenience of ordering many of the requisite reagents to start our syntheses. The just-in-time (JIT) procurement system permits us to have most chemicals at our doorstep within 18 to 24 hours. Even so, detailed planning and logistics go into making sure all reagents and solvents and gases and glassware are ready for a day’s lab work.
Solvents need to be pre-distilled before use since small impurities can promote or catalyze undesired side reactions. Intermediate molecules need to be pre-made and properly stored in a freezer away from light and oxygen to prevent their decomposition while the other segments of the synthesis are being done.
A rich chemical literature provides guidance on reaction types and conditions that are useable on similar molecular constructs, although modifications are almost always needed since the substrates in a new synthesis are different. - Now that I think about it
Reagent addition order is critical. A needs to be added before B, and then C, and each at its own specific temperature to effect a proper reaction and coupling yield. The parameters of temperature, pressure, solvent, light, pH, oxygen, moisture, have to be carefully controlled. Unless one can devise sophisticated promoters or catalysts that are stable in air and moisture and can work at common atmospheric conditions, precise control must be maintained. But making such ambient stable promoters or catalyst is more complex than just varying the temperature for the specific reagent, or putting the reaction in a carefully maintained atmospheric control box (dry-box) equipped with oxygen and moisture sensors, all maintained under a positive pressure of inert nitrogen gas. - It’s not cheap
Once the desired product is synthesized, it can take much longer to properly characterize the product than it did to make it. We use a host of tools, costing millions of dollars, to facilitate rapid molecular structure identification. - In chemistry, everything is hard, time-consuming, and expensive.
Life Lessons for the Prebiotic ChemistCarbohydrates are the backbones of nucleotides, which in turn are needed for DNA and RNA. Carbohydrates also serve as recognition sites for cells to communicate with each other, and as food sources for living systems. The difficulties involved in carrying out carbohydrate synthesis in a prebiotic environment parallel those found in making nanovehicles.
.................
DNA requires a five-carbon sugar, or D-(-)-ribose, one of eight possible pentoses. Blind synthetic pathways lead to a host of products that are unwanted because they are unneeded; and, yet, acting as blindly as Louis Braille, nature somehow found the requisite five-carbon sugar. How?
So far as life goes, as Teacher’s is the great Scotch, water is the great solvent. Nature depends on variations in pH and salinity. Organic synthesis is very hard to do in water. Highly oxygenated organic compounds are needed. The synthetic chemist must project the oxygenated groups out toward the water domain, and project the non-oxygenated groups in toward each other, thus generating a hydrophobic domain. It is very hard to do.
By doing our nanocar organic synthesis in organic solvents rather than in water, we markedly lessened the difficulty; it is a luxury that nature did not (and does not) enjoy. Starting from scratch, she would have had to redesign her structures, discarding the inevitable false starts as they occurred. Whatever else she may have been doing in the prebiotic era, nature was not consulting the modern chemical literature.
Any prebiotic system is destined, at least some of the time, to crash and burn. How does nature know how to stop, or why?
As for the yields of chemical reactions, we design the reactions to minimize diastereomeric mixtures that can be nearly impossible to separate. We try our best to avoid the undesired diastereomers because their separation is too time-consuming and expensive. They waste a huge amount of starting material; they generate unwanted products. Enantiomeric separations are all the more difficult. We avoided that by building a system with only one motor which functioned regardless of whether it turned clockwise or counterclockwise.
Nature has chosen a far harder route, using predominantly one enantiomer (homochiral) in a system with multiple stereogenic centers.
Tough for us, easy for her, strange all around.
.............
Wish FulfillmentFrom a paper on prebiotic chemistry:
Moreover, there was the well-known—but still no less remarkable—fact that in cellular biochemical processes, monosaccharides apparently never operate in the free state, but always in phosphorylated form. It is a short step from such considerations to the notion of a primordial scenario in which, again, phosphorylated and not simply neutral forms of carbohydrates would have been operative [emphasis added]. In a self-organization process in a primordial environment, it may have been of primary importance for carbohydrate molecules to escape chemical chaos, finding themselves instead at concentrations suitable for chemical reactions, and in reaction spaces that would facilitate efficient chemical transformation. With respect to both requirements, phosphorylated sugar molecules would, through their electrical charges, have offered advantages over neutral, water soluble carbohydrates in environments containing mineral surfaces or minerals with expandable layer structures. 37 That short step is not short at all. Biochemical routes are far downstream and occur in far more complex scenarios. In the laboratory, phosphorylation required precise control of phosphorylating agents.
These hopeful but unlikely suggestions pain the synthetic chemist under any circumstance, but for some remarkable reason, they are tolerated in prebiotic chemistry.
Despite claims to the contrary, research on mineral surfaces has done little to solve the problem of overall yields, or that of diastereo- and enantioselectivities. 38 Reagent addition order is critical. An abiogenetic pathway would require several lines of intermediates forming in proximity, and then coming together in the proper order at the precise moment and location needed for synthesis. We could modify many parameters during synthesis: temperature, pressure, solvent type, light, pH, oxygen, moisture. No such controls figure in a prebiotic environment.
Characterization is critical. Without it, impurities accumulate. What prebiotic characterization might mean is anyone’s guess.
Given poor prebiotic reaction yields, it is impossible to envision a process in which the starting materials generate all of the desired products. We had to go back over and over again to generate molecular intermediates, a process known familiarly as “bringing up material from the rear.”
How would prebiotic chemistry bring up its own rear over and over again? It has kept no laboratory notebook to record the previous paths.
In our synthesis, we spent a great deal of time on separation and optimization. If byproducts are permitted to accumulate, they often will consume the new steps’ reagents and alter the course of the reaction.
This problem would plague abiogenesis, too.
It Stands to ReasonThere must have been a chemical means, once upon a time, to generate an information-bearing molecule such as DNA or RNA. Since the 1960s, a number of biologists have suggested that the polymer is RNA rather than DNA. Such is the RNA World Hypothesis. 39 And chemically activated ribonucleotides can polymerize to form RNA. So far so good.
But RNA is far less stable than DNA, and whatever the polymerization, it yields generic RNA, a molecule lacking sequence specificity. Had RNA researchers succeeded in producing a volume of random sentences—subtends flack lachrymose esurient—none of them would have imagined that they had succeeded in composing King Lear.
...............
Sutherland and coworkers pointed out in 2015 that “[a] minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems.” 43 They also acknowledged that, to date, prebiotic chemistry has made ambitious extrapolations: “To imagine the abiotic assembly of such an overall [cellular] system [or subsystem], however, places great demands on hypothetical prebiotic chemistry.” 44 Yet this revealing comment by Sutherland and his coworkers is coupled with their disclosure of a new experimental finding showing
that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of hydrogen cyanide and some of its derivatives … The key reaction steps are driven by ultraviolet light, use hydrogen sulfide as the reductant and can be accelerated by Cu(I)-Cu(II) photoredox cycling. 45 They assert boldly that, “all the cellular subsystems could have arisen simultaneously through common chemistry.” 46 This has now raised the level of suppositions from mere molecule types to complex subsystems where molecules are working in concert toward a common functional goal. But compositions of a few molecule types, or even all of them, do not constitute a cellular subsystem. It is essential to emphasize that the authors only prepared precursors to the ribonucleotides, amino acids, and lipids, not the actual molecules, so the gross extrapolation is all the more disconcerting.
When reading the protocols for the suggested prebiotic-like precursors, one is struck by the high-level sophistication, expert synthetic prowess, and remarkable ingenuity of the researchers. Some reactions were run at room temperature, some at 60°C, others at 100°C and then washed with ice-cold water. Often the molecules prepared by these supposed prebiotic routes were not used, but had to be made more cleanly and in larger scale using purely synthetic methods and organic solvents, such as Lawesson’s reagent and tetrahydrofuran, respectively, “to simplify the handling procedures.”
JIT and precise order of addition protocols were used over and over again. One sees precise pH adjustments through the syntheses, use of ion exchange resins, and separations from the reaction mixtures because proceeding without separations would have destroyed the carefully prepared products. The preparation of cyanoacetylene on Cu(I) was suggested as a way to prepare it conveniently and store it for use when needed. CuCl was mixed with KCl to generate the Nieuwland catalyst, K[CuCl2], at 70°C. Then a separately generated source of acetylene gas was prepared from CaC2 and water. This gas was bubbled through the Nieuwland catalyst to prepare acrylonitrile (an unstable molecule that needs proper isolation and storage to inhibit its polymerization), which was then treated with KCN for 1h, then 5 equivalents of NH3 as a 13 molar NH3/NH4+ solution adjusted to pH 9.2 with NaOH to generate the desired aminopropionitrile.
All of the reactions were executed in separate clean vessels and properly isolated prior to proceeding to the next reaction.
This is just a sampling of preparations that are difficult even for the skilled synthetic chemist to execute. The routes afford very simple precursors to just a few of the many molecules within the building block class, and all their precursors were racemic if they even bore any possible stereoisomerism.
.............
The Current StateThose who think scientists understand the issues of prebiotic chemistry are wholly misinformed. Nobody understands them. Maybe one day we will. But that day is far from today. It would be far more helpful (and hopeful) to expose students to the massive gaps in our understanding. They may find a firmer—and possibly a radically different—scientific theory.
The basis upon which we as scientists are relying is so shaky that we must openly state the situation for what it is: it is a mystery. |
