Molecular Heterogeneous Catalysis, Wiley (2006), 352729662X

368 Chapter 9

In this scheme, catalysis occurs through two molecular recognition steps. One reactant is trapped by a molecular catalytic component which resides in solution and the other reactant is trapped by an immobilized component of the catalyst. The reaction between the two reagents occurs in a self assembled system of the two components, kept together by supramolecular interactions such as hydrogen bonds and van der Waals interactions. The complex decomposes, releasing the product after reaction. Since three molecular recognition events take place, this reaction scheme should be highly selective.

The ultimate catalyst synthesis process is a self organization process in which the catalyst system organizes in situ from catalyst components. Such a process is more complex than proposed in Fig. 9.1, which is designed for a specific reaction with specified reactants. Here we aim at a process analogous to that for zeolite synthesis. In the solution phase there are many di erent oligomers that are able to form well-defined molecular clusters with a particular template. Di erent templates give rise to di erent clusters. The ultimate self organizing catalytic system forms di erent catalyst assemblies depending on the reactant used. In the process in Fig. 9.1, this means that catalyst components A and B self assemble di erently depending on the catalytic reagents. This implies that in addition to molecular recognition, self assembly must also occur. To mimic the biological system, the self assembled catalyst should be able to replicate. In its more elementary form an autocatalytic reaction cycle should follow in which the self assembled system reproduces itself. More generally, this would require a reproductive and self organizing type of reaction system. If as a template for self assembly a molecule is used that is analogous to the reaction transition state, the system should not only self assemble around a template, but should also be able to replicate the template. As discussed in the previous chapter, in the biological combinatorial evolutionary immuno system reaction such a process is actually realized.

The design of catalytic self–organizing cell type systems can be helped by the answers found for the evolutionary origin of metabolic cellular living systems. We will review here our current understanding of the origin of protocellular systems, with a focus on the chemical and physical aspects that relate to catalysis. Such theories imply the evolution of life-like cellular systems from lifeless chemosystems. In the first five sections of this chapter, we will review theories on the generation of protocellular systems. As a followup in later sections we will introduce the application of biomineralization towards the synthesis of mesoporous siliceous systems with a variety of cellular structures related to the siliceous skeleton of diatoms. Biomineralization of catalytic systems is essential chemistry to convert preorganized catalyst precursor assemblies into robust, solid, heterogeneous catalysts.

The history on the theories of the origin of life is extensive. A major advance early in the last century was Pasteur’s demonstration that no life originates spontaneously from lifeless materials. In the same period, W¨ohler synthesized urea from inorganic components, which can be considered the start of organic chemistry. Urea is a molecule that only occurs in living systems. Its synthesis implies that molecules of living systems can be created from the lifeless world. Synthesis from inorganic components of a cell type system mimicking biological cells is a great challenge and would have not only important technological consequences, but would also alter Pasteur’s paradigm. The succesful synthesis of a cellular “living” system would imply that lifeless material can be designed to behave life like. The acceptance that processes exist that spontaneously generate replicating, protocellular systems increases the probability of some kind of life on a planet in another solar system. Several theories and also experiments indicate that the generation

Heterogeneous catalysis the origin of life, biomineralization 369

of life-like systems from lifeless material should be possible.

First, there are the physical models of self organization and reproduction, originating from irreversible thermodynamics as proposed by Prigogine[2]. He discovered the rules for the generation of stable[1] self organized systems cyclic in time and patterned in space far out of equilibrium. A precondition[2] for the stability of such states is mass and energy flow through the system.

Then there are the theories of complex adaptable systems heralded especially by Kau mann[3], that propose that reproductive living cellular systems can be generated once autocatalytic systems have exceeded a particular limit of complexity. These theories refer to reproducing systems, without the need for a template system that act as a code to be replicated for reproduction. The above theories consider self organization and reproduction to be a consequence of complexity. The properties of active media discussed in the previous chapter are related. It has been discussed there that under particular, unique conditions self reproduction and self organization features emerge. In order for a living system to reproduce and convert matter and energy, von Neumann[4] (see also Chapter 8, page 348) proposed the necessity for an algorithmic program that instructs cell operation, as well as the need for hardware in order to execute the program. A reproducing system has to replicate both the instructing code and the hardware. As instructing code we recognize in the biological system the DNA genetic code that replicates in cell multiplication. The hardware of the cell is the proteins that act as the enzymes and thus determine which chemical reaction in a cell is executed.

In addition to the physical theories, there are also several chemical approaches. Here one can broadly distinguish two ways of thinking, that are not only basic to the chemistry one proposes, but also to the physical models one intends to explore. The so-called RNA world view proposes that life has coincided with the origin of the genetic apparatus. The genetic apparatus is the DNA template that controls cell architecture. Eigen and Schuster[5] and also Kuhn and F¨orsterling[6] have developed evolutionary models based on these premises. The alternative view is the Oparin[7] view, which proposes that the origin of first cellular systems coincided with the development of reproducing, self organized metabolic systems, that convert feed molecules to cellular material and waste. Such systems would be applicable as catalytic systems, when feed molecules are also converted into a particular product. This view is also consistent with the models proposed by Prigogine and Kau mann. Reproduction takes place by cell multiplication. In life, reproduction is a necessity because no living system has an infinite existence. We know this well from material science, because materials tend to age and disintegrate with time. This provides a natural reason for the existence of reproduction and, hence, of evolution[8]. Since reproduction is never faultless, some systems will start to reproduce faster than others, depending on system conditions. A process that aims to develop self assembled catalytic systems that are able to adapt to di erent reaction requirements can also exploit evolutionary development by enabling di erent growth rates for particular mutants. As long as the concentrations in the cell system are homogeneously distributed, there is no need for genetic instruction. Genetic reproduction becomes necessary once cellular organization has reached a level of organizational complexity such that it cannot be reproduced directly by cell multiplication.

Evolution within the RNA world stems from copying errors of DNA, that are created upon the reproduction of di erent systems. Several options have been proposed to prevent the so-called error catastrophe that might occur. The error catastrophe is due to the accumulation of errors that gives a progressive deterioration of the system until it is

370 Chapter 9

totally disorganized. To resolve this, Eigen proposed the existence of hypercycles. These are part of a metabolic system coupled to the replicative system that initially exists as quasi-species of the RNA type. The quasi-species undergo a Darwinian process of selection. In a hypercycle several such quasi–species chemically associate with protein enzymes. As Dyson[9] describes, the enzymes associated with one species are supposed to assist the replication of a second quasi-species, and vice versa. The linked populations then become locked into a stable equilibrium. There appear to be additional catastrophes so that the system may yet collapse. Short circuits may occur minimizing the cycle, or a single RNA may multiply too e ciently and become a parasite, choking the rest of the population to death. There is also the possibility of statistical collapse, when one of the components of a cycle disappears. There appears to be a narrow range of oligomer population size for which the hypercycle acquires an ample, but finite, lifetime.

We will focus on the chemical proposals here in addition to computational models for evolutionary formation of metabolic cellular systems that do not yet have a genetic apparatus. Because of its very general nature, however, we will summarize first an important model of Kuhn on the evolutionary development of the genetic apparatus. We have selected this more generally applicable model because it highlights some key chemical principles for evolutionary reproduction. According to Kuhn, design principles for fabricating supramolecular systems are:

–Lock and key molecular recognition related concepts.

–Programmed environment change concept.

Supramolecular systems are aggregates held together by weak chemical interactions such as hydrogen bonds or van der Waals interactions. We recognize them in cellular systems as the aggregates formed by macromolecules. Supramolecular systems are also fundamental to self assembly and molecular recognition systems as we discussed above. The lock and key concept, and variations on it as we discussed in this book, are the basis of molecular recognition and catalytic selectivity. The need for a programmed environment refers to identifying the conditions that lead to the evolution of life-like systems at the end of a long sequence of consecutive steps.

For the formation of macromolecular chains from a limited number of monomers, Kuhn proposed the following aspects as important for the environment of the developing system, aspects that we also will recognize in chemical model systems:

-A spatial and temporal structure has to be present in special locations. For instance, a microporous spatial structure in a rock structure helps by maintaining a high concentration of molecules, to enable the initial start of a cycle of multiplication of simple strands of oligomer molecules. Energy-rich building blocks should be available. Self organization decreases entropy, which is only possible when energy is consumed.

-Microdiversity of the environment serves as an evolutionary gradient. Neighborhood regions with slightly di erent structural properties cannot be populated in the beginning but later by casually occurring slightly improved chemical systems.

The evolution of early life according to Kuhn can be summarized as follows. Initially under prebiotic conditions, the building blocks amino acids, nucleotides and lipids were formed. An autocatalytic replication mechanism of oligomers is proposed. The above-mentioned environmental changes lead to supramolecular engineering of simple living cells, through self-learning, evolutionary, adaptive processes.

Computational methods such as the genetic algorithms discussed in Chapter 8 have

372 Chapter 9

Chapter 8. We argued earlier that this can be considered a combinatorial process based on template recognition. Prior to zeolite crystallization aggregates are formed, of the size of a few nanometers, specific for each zeolite. These intermediate aggregates may serve the same role as Kuhn’s oligomeric aggregates. They may enhance the formation of these siliceous oligomers that are the elementary building units from which the crystal is to be formed.

(c)In order to create an interior separate from the environment, an envelope has to develop around the aggregates, leading to confinement of the building blocks. Liposomes, that are bounded by membranes, can be considered examples.

(d)In order to minimize error accumulation in a replicating system with increasing complexity, a translation device, that relates membrane development to the replicating molecules, has to develop, as part of the envelope-forming apparatus. This, according to Kuhn, is the RNA–DNA machinery. However, as we will see for a homogeneous system of limited complexity, such a machinery may not be necessarily needed.

Russell et al.[11] and W¨achtersh¨auser[10] have proposed a very important chemical realization of a system close to the Kuhn model. Di erently from the Kuhn model, Russell and W¨achtersh¨auser focus on the generation of a self assembled, reproducing metabolic cellular system, that does not yet contain a genetic reproducing hereditary system. They propose that the initial protocell system was inorganic and prebiotic reactions were of a heterogeneous catalytic nature. The generation of enzymes and organic membranes is a later system evolutionary step. Both authors proposed that protocellular life emerged initially at sulfidic submarine springs, in a stage of the evolution of the Earth where the atmosphere was largely reducing. Typical conditions are an atmosphere of 10 bar, the presence of CO2 and CO, with some CH4 and NH3 and of course water. Energybuilding materials proposed by W¨achtersh¨auser’s scheme are those reagents which drive pyrite-forming reactions such as:

(n + 1)CO2 + 3nFeS + 3nH2S −→ HO(CH2)nCOOH + 3nFeS2 + (2n − 1)H2O Alternatively, photochemical reactions may have been important;

4H+ + 2Fe(OH)+ hν 2Fe3+ + 2H O + H

−→ 2 2

The hydrogen produced is used to form lipophylic molecules in catalytic chain growth reactions. W¨achtersh¨auser[12] proposed that chain growth would occur initially through a so-called archaic reductive citric acid cycle in which SH groups coexist with OH groups and carbonyl groups coexist with this derivative. The archaic citric acid is autocatalytic in the succinate intermediate that is formed by the incorporation of four CO2 molecules. Hydrogen and energy are produced by the ferrosulfide reaction with H2O to give pyrite.

Cairns-Smith and Walker[13] propose reaction networks in which formaldehyde and glycolaldehyde are key intermediates. The di erent networks are considered phenotypes, formed by catalytic contact with clay minerals. Clays are proposed to play a role similar to DNA in replication. Replicating clays are thought to contain the “genetic information” (cation composition, distribution, imperfections, etc.) for pre-life metabolic systems.

Membrane growth at sulfide mounds can occur at the interface between iron-deficient, HS-bearing and thiolate (RS)−-bearing alkaline (pH 8) reduced hot spring water and iron-bearing, mildly oxidized and acidic (pH 5) ocean[14]. Traces of tungsten and molybdenum may be present. W¨achtersh¨auser also pointed out that initial reactions should have

occurred as surface reactions on the iron–sulfide surface, since a closed membrane would not allow for the di usion of reactant molecules into the quasi-cellular system. Attachment to the surface also concentrates surface reaction intermediates so that long-chain molecules can be formed in a chain-growth type process. Once lipophilic molecules are formed they will envelop the pyrite particles. In the process, the sulfide particles may decompose and actually become incorporated into the lipophilic membrane. This provides an interesting evolutionary path to the generation of enzymes, from the initially heterogeneous sulfide system. The membrane molecules may become ligands of the metal sulfide cationic clusters. This will begin to introduce catalytic selectivity and now peptide molecules may be formed from reactions with NH3 produced by catalytic reactions with

N2 and H2. Hydrothermal conditions have been identified under which NH3 is produced from N2[15].

Initial pre-life reproducing cellular systems emerge as a membrane-bonded vesicle incorporating autocatalytic enzyme-type catalysts. There is an ongoing metabolic process that lead to cell growth and cell multiplication. Evolutionary adaptive systematics leads to cell growth and cell death, depending on the relative value of di erent reaction parameters. Computational models of such processes are discussed in Sections 9.3 and 9.4.

9.2 The Origin of Chirality

There are many speculations on the origin of chirality of biosystems. Most interesting for the self assembly of reproducing catalytic systems are theories on the amplification of enantiomeric excess. Frank[16] proposed a general mechanism for spontaneous asymmetric synthesis. He showed that if the production of living molecules of life is rare and, hence, slow compared with their rate of multiplication, the whole Earth is likely to be extensively populated with the progeny of the first event before another appears. A living entity is defined as one able to reproduce its own kind. Frank showed that a simple and su cient life model is a chemical substance which is a catalyst for its own production (hence, autocatalytic) and an anticatalyst for the production of its optical enantiomers.

Rate events are fluctuations and statistical averaging requires a large number of them. If the time scale of averaging is long compared with the amplification of the fluctuations, symmetry breaking occurs and one enantiomer dominates. This view is in line with mathematical analysis[17] which shows that macroscopic behavior derived from collective dynamics of microscopic components cannot be modeled using spatially continuous density functions. One needs to take into account the actual individual/discrete character of the microscopic components of the system.

Bonner[18] concluded that e cient polymerization mechanisms that involve enantioselective enrichment via α-helix or β-sheet secondary structures during polypeptide growth, are applicable to prebiotic environments. Total spontaneous resolution of racemates during crystallization involving secondary asymmetric transformations can also be important. The polymerization amplification concept involves the partial polymerization of a slightly enriched amino acid mixture, followed by an autocatalytic sequence of additional partial hydrolysis and polymerization steps. These amplification reactions occur because reactions of one enantiomer with another to form two diastereomeric products occur at di erent rates for each diastereomer.

Wynberg[19] suggested that the enantiomeric form of the chiral autocatalytic products might be able to form semi-stable dimer complexes, resulting in enrichment of the uncomplexed catalytic product. Experimental proof was given[20] that enantiomerically

374 Chapter 9

enriched alkali metal alkoxides, which can give aggregates in solution with both products and reactants, can act as chiral catalysts for their own formation from achiral reactants, yielding a product with enhanced excess enantiomeric selectivity of the same chirality.

Breaking of symmetry has been reported in stirred[21] crystallization. NaClO3 crystallization in an unstirred solution produces a statistically equal number of l- or d-crystals, but crystallization in a stirred achiral solution can produce 99% crystal enantiomeric excess. This is due to a secondary nucleation phenomenon. Dendritic or needle-like structures on the surface of a crystal break o in a stirred solution. The result is an amplification of the corresponding enantiomeric phase.

9.3 Artificial Catalytic Chemistry

Kau mann defined a living system as a physical cell able to self reproduce and at least able to complete a single thermodynamic cycle that executes work. A minimal model of primitive self maintaining cells named chemoton was defined by Ganti [22]. It is composed of:

(1)a metabolic system of autocatalytic molecules;

(2)self replicating molecules that inherit genetic information;

(3)a self organizing membrane molecule to enclose the system.

Since the production of a membrane costs energy, a reaction cycle is required that generates energy and allows its use in the production cycle. External resources are used as an energy source and as building materials of the protocell and partially converted to waste. The artificial catalytic cell would be selective in its waste production and produce instead desired products.

The di erent reaction cycles often require di erent conditions. This generates a need for compartmentalization with communication between compartments.In modern cells, electrocatalytic processes with the consumption and generation of electrons and protons and their transport through membranes play an important role in this respect. The system operates far from equilibrium, where cyclic behavior can be maintained.

Kau mann demonstrated that chemical reaction networks that exceed a minimum requirement of complexity convert to a state of self reproduction coupled to a production cycle. With increasing complexity, the system undergoes a phase transition from a disordered, non-reproducing state to a self-organizing and self-reproducing state. It follows from the previous paragraph that there is also an upper limit to this complexity, beyond which a genetic apparatus becomes necessary for reproduction.

Several computational models have been designed to analyze the evolution of self organization of the first protocell. The supporting growth processes are evolutionary, combinatorial process sequences based on a selection principle. In in Chapter 8, we discussed active media that show under particular conditions self organization or chaotic behavior. An evolutionary, combinatorial process leads to the formation or selection of a particular functional material, as a catalyst, by a response reaction with the template. Adaptation implies that the multiplying system develops altered properties due to a Darwinian selection process. Combinatorial processes make adaptation possible. Once a replication principle is operational, mutation by errors occurs and self-correction mechanisms also have to be present. We will summarize these concepts by discussing here the Graded Autocatalysis Replication Domain (GARD) model and Lattice Artificial Chemistry model.

Heterogeneous catalysis the origin of life, biomineralization 375

9.3.1 Graded Autocatalysis Replication Domain Model

An important question is whether a rudimentary genetic memory may emerge based on statistical rules of mutually interacting catalytic reaction networks. The basic idea of such a compositional genome is that in a mixture of relatively simple chemicals, the array of relevant concentrations may be viewed as a vehicle of information storage. According to Morowitz[23a], memory can also exist without specific macromolecules, but may be initiated in a chemical network with catalytic loops and reflexive autocatalysis in which the same catalyst participates in di erent networks.

In biological systems, memory [the genetic apparatus) and operating system (the catalytic enzymes organized into (auto)catalytic networks], are distinguished. According to the Oparin model, in very early life these may not have been separated. Morowitz defined a boundary for molecular assembly to ensure its compositional inheritance (see Fig. 9.3). If an assembly contains m molecular species and if each is present with an average copy number 2r per assembly, then the probability that all molecular types are present in the progeny in at least one copy is given by P b = (1 - e−r )m . r is to be interpreted as the number of (autocatalytic) reaction paths that interconnect the di erent molecular species. When the number of molecules increases, r scales with a power of m.

The Morowitz boundary is defined as P b = 0.5. At large values of r, P b approximates 1 and the system reproduces. One can consider this to be due to the redundancy of the system, so that upon replication the key autocatalytic cycles are easily transmitted.

The model systems described so far belong to the class of the so-called Replicative– Homeostatic Early Assemblies (RHEA). The concept of homeostasis and the idea of self replication stems from Oparin: “..... the stationary drop of a coacervate (particle enclosed by a membrane), or any other open system, may be preserved as a whole for a certain time while changing continually in regard to both its composition and the network of processes taking place within it, always assuming that these changes do not disturb its dynamic stability”.

The GARD model assumes combinatorial or random chemistry with random emergence of diverse organic molecules. The transition from random chemistry to self-replicating entities occurs because of intrinsic statistical factors. A key step is the definition of a matrix for random catalytic interactions, which may be based on molecular recognition within random receptor assemblies. The GARD model assumes a finite enclosure (e.g. an amphiphilic vesicle), containing the catalytic set of members, and absorbing energyrich chemical precursors from the external environment. Computational implementation occurs by numerical solution of di erential equations or by Monte Carlo simulations.

In the Lattice Artificial Chemistry model and also in later extensions of the GARD model, formation of the membrane itself is explicitly included. In GARD every species Aj may, in principle, catalyze every possible reaction in which another species Ai is formed/decomposed, with a catalytic probability βij . This β matrix defines the chemical structure of the (auto)catalytic networks. The role and formation of the amphiphilic assembly that becomes the enclosing membrane can be incorporated into the catalytic network by assuming that the same molecules that form the assembly are also responsible for the mutually catalytic functions. This is a model that contains similarities with the sulfide protocell systems discussed earlier. The results of numerical simulations based on extended GARD model versions demonstrated the spontaneous emergence of catalytical assemblies that tend to lie below the Morowitz boundary.

In the above models, interest was focused on evolutionary system development to