Serine octamers: cluster formation, reactions, and implications for biomolecule homochirality

The emergence of homochirality continues to be one of the most challenging topics associated with the origin of life. One possible scenario is that aggregates of amino acids might have been involved in a sequence of chemical events that led to chiral biomolecules in self-replicating systems, that is, to homochirogenesis. Serine is the amino acid of principal interest, since it forms "magic-number" ionic clusters composed of eight amino acid units, and the clusters have a remarkable preference for homochirality. These serine octamer clusters (Ser8) can be generated under simulated prebiotic conditions and react selectively with other biomolecules. These observations led to the hypothesis that serine reactions were responsible for the first chiral selection in nature which was then passed through chemical reactions to other amino acids, saccharides, and peptides. This Review evaluates the chemistry of Ser8 clusters and the experimental evidence that supports their possible role in homochirogenesis.     

Formation and stability of charged amino acid clusters and the role of chirality

Amino acid clusters have been studied by several groups and most notably magic number clusters and chiral recognition have been reported. In this work, we have studied the formation of amino acid clusters by electrospray ionization (ESI) and their stability by high-energy collision-induced dissociation (CID). Appearance sizes were determined for multiply charged clusters where the charge is either due to protons or to sodium ions. Finally, we conclude that chiral selectivity plays an important role in cluster formation but seems to be of minor importance for the fragmentation of mixed clusters.     

Formation of the serine octamer: Ion evaporation or charge residue

The mechanism of formation for clusters of serine generated by electrospray ionization is hypothesized to play a critical role in determining their ultimate properties. Under carefully manipulated electrospray source conditions, two distinct and well-separated distributions of clusters can be observed. The characteristics of the two cluster populations are consistent with different formation mechanisms, namely ion evaporation and charge residue. Upon further inspection, it is proposed that the magic number intensity, homochiral selectivity, and unique formation of the serine octamer are best explained within the context of the ion evaporation mechanism. As a consequence, solution phase properties of the octamer become important, particularly in relation to interface effects present on the surface of the charged droplet. In contrast, other clusters of serine, including the B form of the octamer, are probably generated by the charge residue mechanism and may have no connection to condensed phase phenomena.     

Chiral enrichment of serine via formation,dissociation, and soft-landing of octameric cluster ions

Chiral enrichment of serine is achieved in experiments that involve formation of serine octamers starting from non-racemic serine solutions. Serine octamers were generated by means of electrospray and sonic spray ionization of aqueous solutions of d(3)-L-serine (108 Da) and D-serine (105 Da) having different molar ratios of enantiomers. A cyclic process involving the formation of chirally-enriched octameric cluster ions and their dissociation, viz. Ser(1) --> Ser(8) --> Ser(1), allows serine monomers to be regenerated with increased enantiomeric excess as shown in two types of experiments: (1) Chiral enrichment in serine was observed in MS/MS/MS experiments in a quadrupole ion trap in which the entire distribution of serine octamers formed from non-racemic solutions was isolated, collisionally activated, and fragmented. Monomeric serine was regenerated with increased enantiomeric excess upon dissociation of octamers when compared with the enantiomeric composition of the original solution. (2) Chiral enrichment was observed in the products of soft-landing of mass-selected protonated serine octamers. These ions were generated by means of electrospray or sonic spray ionization, mass selected, and collected on a gold surface using ion soft-landing. Chiral enrichment of the soft-landed serine was established by redissolving the recovered material and comparing the intensities of protonated molecular ions of d(3)-L-serine and D-serine after APCI-MS analysis. Both of these experiments showed comparable results, suggesting that formation of serine octamers depends only on the enantiomeric composition of the serine solution and that the magnitude of the chiral preference is intrinsic to octamers formed from solutions of given chiral composition.     

Thermal formation of homochiral serine clusters and implications for the origin of homochirality

Spontaneous assembly of amino acids into vapor-phase clusters occurs on heating the solid compounds in air. In comparison to the other amino acids, serine forms clusters to an unusual extent, showing a magic number octamer on sublimation; this octamer can be ionized and characterized by mass spectrometry. Two isomers of the vapor-phase serine octamer are generated, the minor one at 130 degrees C and the major at 220 degrees C. The higher temperature cluster shows a strong homochiral preference, as confirmed by isotopic labeling experiments. This serine cluster, like that generated earlier from solution in electrospray ionization experiments, undergoes gas-phase enantioselective substitution reactions with other amino acids. These reactions transfer the chirality of serine to the other amino acid through enantioselective incorporation into the octamer. Other serine pyrolysis products include alanine, glycine, ethanolamine, and small dipeptides, and many of these, too, are observed to be incorporated into the thermally formed serine octamers. Chiral chromatographic analysis confirmed that L-serine sublimation produced DL-alanine, glycine, and ethanolamine, while in the presence of hydrogen sulfide, L-serine yielded L-cysteine. The data demonstrate that sublimation of serine under relatively mild conditions yields chirally enriched serine octamers and that the chiral preference of the starting serine can be transferred to other compounds through cluster-forming chemical reactions.     

From achiral porphyrins to template-imprinted chiral aggregates and further. Self-replication of chiral memory from scratch

The presence of 10-13 M of chiral clusters of aromatic amino acids addresses aggregation of opposite-charged achiral porphyrin towards the formation of smart chiral assemblies. The latter supramolecular complexes are able to self-propagate and transfer their chiral information with a 100% yield. The chiral bias occurs through a correlated sequence of induction, memory, and amplification of chirality that strongly recalls possible prebiotic scenarios.     

Chirality transfer from a single chiral molecule to 2D superstructures in alaninol on the Cu(100) surface

The formation of 2D chiral monolayers obtained by self-assembly of chiral molecules on surfaces has been widely reported in the literature. Control of chirality transfer from a single molecule to surface superstructures is a challenging and important aspect for tailoring the properties of 2D nanostructures. However, despite the wealth of investigations performed in recent years, how chiral transfer takes place on a large scale still remains an open question. In this paper we report a coupling of scanning tunneling microscopy and low energy electron diffraction measurements with an original theoretical approach, combining molecular dynamics and essential dynamics with density functional theory, to investigate self-assembled chiral structures formed when alaninol adsorbs on Cu(100). The peculiarity of this system is related to the formation of tetrameric molecular structures which constitute the building blocks of the self-assembled chiral monolayer. Such characteristics make alaninol/Cu(100) a good candidate to reveal chiral expression changes. We find that the deposition of alaninol enantiomers results in the formation of isolated tetramers that are aligned along the directions of the substrate at low coverage or when geometrical confinement prevents long-range order. Conversely, a rotation of 14° with respect to the Cu(100) unit vectors is observed when small clusters of tetramers are formed. An insight to the process leading to a 2D globally chiral surface has been obtained by monitoring molecular assemblies as they grow from the early stages of adsorption, suggesting that the distinctive orientation of the self-assembled monolayer originates from a balance of cooperating forces which start acting only when tetramers pack together to form small clusters.     

Origin of chiral selectivity in gas-phase serine tetramers

Serine "magic-number" clusters have attracted substantial experimental and theoretical interest since their discovery. Serine undergoes marked chiral enrichment upon sublimation, which has been associated with the homochiral selectivity of the octamer. This process has been implicated in one possible mechanism leading to the origin of biological homochirality. While the octamer is the best known of the serine clusters, here we focus on the tetramer, the smallest serine cluster known to exhibit homochiral preference. This choice is based on its greater simplicity and tractability with accessible computational resources. Basin-hopping molecular dynamics simulations coupled to density functional theory calculations yield a "structural landscape" for low-lying configurations on the potential energy surface. The full range of enantiomeric compositions and charge states is investigated. Global energy minimum serine tetramers consist of a cage structure bonded by zwitterionic terminal groups. The participation of the serine hydroxyl side chains in hydrogen bonds with adjacent monomers drives the homochiral selectivity of serine tetramers. The configuration of the hydrogen bonding network is strongly dependent on enantiomeric composition and charge state. Smaller cations are incorporated into the center of the tetramer cage and effectively disable all side chain hydrogen bonding, while larger cations appear not to incorporate into the tetramer cage and are stabilized outside only in the homochiral case. The current theoretical data requires the introduction of a kinetic barrier to complete the model, limiting rearrangement from the basic cage configuration in some cases, which is discussed and probed directly by doubly-nudged elastic band transition state searches. These calculations elucidate a large barrier for reorganization of the cage, completing the theoretical understanding of the tetramers.     

Letter: some more aspects of formation and stability of the protonated serine octamer cluster

The formation of protonated serine octamer clusters from homochiral and heterochiral monomer solutions was investigated. The well-established preference for homochiral cluster formation was found to originate from collision-induced dissociation of the less stable ion population B prior to reaching the mass spectrometer's analyzer cell. In addition, collision-induced dissociation experiments were undertaken to investigate the relative stabilities of populations A and B and infrared multi-photon dissociation experiments addressed the relative stabilities of the protonated serine octamer cluster and its metaclusters. Isotopically-labeled serine was used throughout the experiments.     

Do homochiral aggregates have an entropic advantage?

The present work seeks to illuminate the underlying principles which control the aggregation of chiral building blocks into larger aggregates by examining the role that entropy plays in this process. Entropic effects are first examined within the confines of a simple model system, and the results are then compared to experimental data on clusters of amino acids. The model system predicts that the formation of a specific structure is more likely to occur from an enantiopure solution because forming a particular structure from a racemic solution is hindered by significant entropic barriers. These predictions are in good agreement with the experimental results. In our examination of clusters of all of the amino acids, clusters which are unusually abundant are found only when enantiopure solutions are sampled. Furthermore, the majority of all clusters exhibit no preference for chiral composition, suggesting that entropic effects negate any changes in enthalpy. Although the experimental data are not comprehensive, our results strongly suggest that specificity in homochiral clusters is entropically advantageous compared to specificity in racemic clusters.     

Chiral separation: mechanism modeling in two-dimensional systems

Fluid phase separations of racemates are difficult because the subtle, short-ranged differences in intermolecular interactions of like and unlike pairs of chiral molecules are typically smaller than the thermal energy. A surface restricts the configurational space available to the pair of interacting molecules, thus changing the effective interactions between them. Because of this restriction, a surface can promote chiral separation of mixtures that are racemic in bulk. In this paper, we investigate chiral symmetry breaking induced by an achiral surface in a racemate. A parallel tempering Monte Carlo algorithm with tempering over the temperature domain is used to examine the interplay between molecular geometry and energetics in promoting chiral separations. The system is restricted to evolve in two dimensions. By controlling the balance between electrostatic and steric interactions, one can direct the surface assembly of the chiral molecules toward formation of small clusters of identical molecules. When molecular shape asymmetry is complemented by dipolar alignment, chiral micellar clusters of like molecules are assembled on the surface. We examine the case of small model molecules for which the two-dimensional restriction of the pair potential is sufficient to induce chiral segregation. An increase in molecular complexity can change the balance of intermolecular interactions to the point that heterochiral pairs are energetically more favored. In this case, we find conditions in which formation of homochiral micelles is still achieved, due to a combination of multibody and entropic effects. In such systems, an examination of the pair potential alone is insufficient to predict whether the multimolecular racemate will or will not segregate.     

Negatively-charged halide adducts of homochiral serine octamers

Negatively charged halide adducts of serine octamers, (Ser(8)+2Cl)(2-) and (Ser(8)+2Br)(2-), appear as magic number clusters in the negative ion electrospray mass spectra of solutions containing serine and the halide. Like the well-known protonated serine octamer, these negatively charged adducts are formed with homochiral preference and also undergo chiroselective substitution reactions with other amino acids. Tandem mass spectra of negatively charged halide adducts of serine octamers show that these ions also have a characteristic fragmentation signature. The fact that octamers of both polarities display analogous chemical properties suggests that these may be characteristics of the so-far-unknown neutral octamer. If serine played a key role in the origin of homochirality on the primitive earth, it was likely through both the neutral octamer and the ionic adducts. Unlike the octamers, the formation of halide-containing serine cluster ions of particular sizes is unfavorable under the conditions of the experiment. Signals corresponding to the ions (Ser(9)+2Br)(2-) and (Ser(15)+2Br)(2-) are particularly low in intensity, giving rise to gaps in the distribution of serine/bromide clusters in the negative ion electrospray mass spectra. These cluster sizes are likely to correspond to unstable "anti-magic number" clusters recently reported by Clemmer.     

Directed Self‐Assembly Pathways of Active Colloidal Clusters

Despite the mounting interest in synthetic active particles, too little is known about their assembly into higher‐order clusters. Here, mixing bare silica particles with Janus particles that are self‐propelled in electric fields, we assemble rotating chiral clusters of various sorts, their structures consisting of active particles wrapped around central “hub” particles. These clusters self‐assemble from the competition between standard energetic interactions and the need to be stable as the clusters rotate when the energy source is turned on, and fall apart when the energy input is off. This allows one to guide the formation of intended clusters, as the final structure depends notably on the sequence of steps in which the clusters form.     

Global and local expression of chirality in serine on the Cu{110} surface

Establishing a molecular-level understanding of enantioselectivity and chiral resolution at the organic-inorganic interfaces is a key challenge in the field of heterogeneous catalysis. As a model system, we investigate the adsorption geometry of serine on Cu{110} using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The chirality of enantiopure chemisorbed layers, where serine is in its deprotonated (anionic) state, is expressed at three levels: (i) the molecules form dimers whose orientation with respect to the substrate depends on the molecular chirality, (ii) dimers of L- and D-enantiomers aggregate into superstructures with chiral (-1 ?2; 4 0) lattices, respectively, which are mirror images of each other, and (iii) small islands have elongated shapes with the dominant direction depending on the chirality of the molecules. Dimer and superlattice formation can be explained in terms of intra- and interdimer bonds involving carboxylate, amino, and β-OH groups. The stability of the layers increases with the size of ordered islands. In racemic mixtures, we observe chiral resolution into small ordered enantiopure islands, which appears to be driven by the formation of homochiral dimer subunits and the directionality of interdimer hydrogen bonds. These islands show the same enantiospecific elongated shapes those as in low-coverage enantiopure layers.     

Detection of Serine Octamer by Desorption Electrospray Ionization Mass Spectrometry in Resultant Mixture of Aspartic Acid Exposed to Sunshine Under Natural Conditions

Serine,one of the nonessential amino acids,is of principal interest because of its capability to form magic-number ionic clusters,which provide a remarkable preference for homochirality.With L-aspartic acid as the precursor,this study provides experimental evidence for serine formation in weak acidified aqueous solutions in the presence of iron,with exposure to sunlight,which simulates the natural conditions of the prebiotic aqueous environment.The resultant mixture is directly analyzed via desorption electrospray ionization mass spectrometry(DESI-MS),without any sample preseparation.The serine monomer is successfully detected as protonated molecules,giving a peak at m/z 106,which is confirmed by the MS/MS fragments.Protonated serine octamer(m/z 841)is also observed with significant abundance in the MS spectra and is confirmed by the MS/MS data,which shows the formation of the serine octamer by a synthesized serine in the resultant mixture.It is also found that the serine octamer yielded equivalent abundance in the DESI mass spectra in a wide pH range(pH=1-5),and that existence of ferrous salt and sunshine are essential for the conversion of aspartic acid to serine in the acidic water solution.     

非手性的棒状分子在非手性表面形成的风车团簇

利用低温STM研究了非手性的棒状并五苯分子在Bi（111）表面形成的手性风车团簇.在团簇内部,并五苯分子分别沿Bi（111）的3个对称轴方向平行排列,形成6个不同的分子带.在每个分子带中,相邻分子之间有一个滑移错位.当平行排列的分子数多于4时,滑移错位发生反向,形成弯曲的风车扇叶.我们认为,分子的滑移错位来自于分子之间的π-π相互作用;而滑移错位的反向是团簇内部的吸引力导致的密堆积的结果.这两种作用的竞争是形成手性风车团簇的微观机制.     

Theoretical evidence for pyramidalized bicyclic serine enolates in highly diastereoselective alkylations

A new chiral serine equivalent and its enantiomer have been synthesized from (S)- and (R)-N-Boc-serine methyl esters (Boc: tert-butyloxycarbonyl). The use of these compounds as chiral building blocks has been demonstrated in the synthesis of alpha-alkyl alpha-amino acids by diastereoselective potassium enolate alkylation reactions and subsequent acid hydrolyses. Theoretical studies were performed to elucidate the stereochemical outcome of both the formation of five-membered cyclic N,O-acetals and the subsequent alkylation process, which occurs with total retention of configuration. This feature could be explained in terms of the high degree of pyramidalization of enolate intermediates.     

Single-Layered Chiral Nanosheets with Dual Chiral Void Spaces for Highly Efficient Enantiomer Absorption

Although considerable effort in recent years has been devoted to the development of two-dimensional nanostructures, single-layered chiral sheet structures with a lateral assembly of discrete clusters remain elusive. Here, we report single-layered chiral 2D sheet structures with dual chiral void spaces in which discrete clusters of planar aromatic segments are arranged with in-plane AB order in aqueous methanol solution. The chirality of the sheet is induced by the slipped-cofacial stacks of rectangular plate-like aromatic segments in the discrete clusters which are arranged laterally with up and down packing, resulting in dual chiral void spaces. The chiral nanosheets function as superfast enantiomer separation nanomaterials, which rapidly absorb a single enantiomer from a racemic mixture with greater than 99 % ee.     

Determination of D,L‐serine in midbrain of Parkinson's disease mouse by capillary electrophoresis with in‐column light‐emitting diode induced fluorescence detection

A capillary electrophoresis method with in‐column light‐emitting diode induced fluorescence detection is described for simultaneous determination of D ,L ‐serine in the midbrain of a Parkinson's disease mouse. D ,L ‐Serine was derivatized with fluorescein isothiocyanate, and chiral separation and determination of D ,L ‐serine derivatives were performed on a laboratory‐built capillary electrophoresis system with in‐column light‐emitting diode induced fluorescence detector using γ‐cyclodextrin as chiral selector. Using this method, the levels of D ‐ and L ‐serine in the midbrains of Parkinson's disease mice were determined. When compared to controls, the levels of D ‐ and L ‐serine showed significant differences. The result suggested that the biosynthesis and the transportation of endogenous D ,L ‐serine may participate in Parkinson's disease pathogenesis.     

Single‐Layered Chiral Nanosheets with Dual Chiral Void Spaces for Highly Efficient Enantiomer Absorption

Although considerable effort in recent years has been devoted to the development of two‐dimensional nanostructures, single‐layered chiral sheet structures with a lateral assembly of discrete clusters remain elusive. Here, we report single‐layered chiral 2D sheet structures with dual chiral void spaces in which discrete clusters of planar aromatic segments are arranged with in‐plane AB order in aqueous methanol solution. The chirality of the sheet is induced by the slipped‐cofacial stacks of rectangular plate‐like aromatic segments in the discrete clusters which are arranged laterally with up and down packing, resulting in dual chiral void spaces. The chiral nanosheets function as superfast enantiomer separation nanomaterials, which rapidly absorb a single enantiomer from a racemic mixture with greater than 99 % ee.