Alkali metal-cationized serine clusters studied by sonic spray ionization tandem mass spectrometry

Serine solutions containing salts of alkali metals yield magic number clusters of the type (Ser(4)+C)(+), (Ser(8)+C)(+), (Ser(12)+C)(+), and (Ser(17)+2C)(+2) (where C = Li(+), Na(+), K(+), Rb(+), or Cs(+)), in relative abundances which are strongly dependent on the cation size. Strong selectivity for homochirality is involved in the formation of serine tetramers cationized by K(+), Rb(+), and Cs(+). This is also the case for the octamers cationized by the smaller alkalis but there is a strong preference for heterochirality in the octamers cationized by the larger alkali cations. Tandem mass spectrometry shows that the octamers and dodecamers cationized by K(+), Rb(+), and Cs(+) dissociate mainly by the loss of Ser(4) units, suggesting that the neutral tetramers are the stable building blocks of the observed larger aggregates, (Ser(8)+C)(+) and (Ser(12)+C)(+). Remarkably, although the Ser(4) units are formed with a strong preference for homochirality, they aggregate further regardless of their handedness and, therefore, with a preference for the nominally racemic 4D:4L structure and an overall strong heterochiral preference. The octamers cationized by K(+), Rb(+), or Cs(+) therefore represent a new type of cluster ion that is homochiral in its internal subunits, which then assemble in a random fashion to form octamers. We tentatively interpret the homochirality of these tetramers as a consequence of assembly of the serine molecules around a central metal ion. The data provide additional evidence that the neutral serine octamer is homochiral and is readily cationized by smaller ions.     

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.     

Spontaneous anti-resolution in heterochiral clusters of serine

Chirality plays an important role in the formation and stability of noncovalent clusters which are made of chiral molecules. It is shown that clusters can exhibit a preference for both homochirality and heterochirality. Serine cluster formation is dominated by the formation of heterochiral aggregates, with the exception of the previously observed homochiral serine octamer. Thus, the majority of serine clusters lead to chiral anti-resolution, or the racemic mixing of enantiomers.     

Spectroscopic Evidence for Clusters of Like‐Charged Ions in Ionic Liquids Stabilized by Cooperative Hydrogen Bonding

Direct spectroscopic evidence for hydrogen‐bonded clusters of like‐charged ions is reported for ionic liquids. The measured infrared O?H vibrational bands of the hydroxyethyl groups in the cations can be assigned to the dispersion‐corrected DFT calculated frequencies of linear and cyclic clusters. Compensating the like‐charge Coulomb repulsion, these cationic clusters can range up to cyclic tetramers resembling molecular clusters of water and alcohols. These ionic clusters are mainly present at low temperature and show strong cooperative effects in hydrogen bonding. DFT‐D3 calculations of the pure multiply charged clusters suggest that the attractive hydrogen bonds can compete with repulsive Coulomb forces.     

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.     

Amino acid cluster formation studied by electrospray ionization mass spectrometry

The association properties of natural and non-natural amino acids were studied in detail using electrospray ionization mass spectrometry. The results show a highly diverse cluster formation behavior of amino acids. There are differences regarding the degree of clustering (average cluster size), the presence or absence of one or several 'magic' clusters of special stability and the influence of chirality on cluster stability. Cluster formation does not show a good correlation with simple physico-chemical properties (such as solubility), indicating that it is a specific process and not only a simple aggregation during evaporation/ionization. A systematic study of cluster formation of serine derivatives reveals that all functional groups play a prominent role in the binding of the magic octamer. The results support the idea of the zwitterionic character of the octamer. Electrospray ionization of the side-chain acetylated serine shows the formation of a very stable tetramer with a strong preference for homochirality. The results suggest that Ser8 is made up of two tetramer subunits, held together by hydrogen bonds of the side-chain.     

Size-selected methyl lactate clusters: fragmentation and spectroscopic fingerprints of chiral recognition

A comprehensive experimental study of the OH stretching vibrations of size-selected clusters of enantiopure and racemic methyl lactate is presented. For the size selection, we measured angular dependent mass spectra and time-of-flight distributions at the different fragment masses. In this way the fragmentation of these clusters upon electron impact ionization is obtained. The largest fragment masses of the neutral (MLac)n clusters are the protonated (MLac)n-1H+ ions. The results of a pressure dependent study in an FTIR jet experiment are compared with completely size-selected experiments based on atomic beam deflection and depletion spectroscopy. The size assignments and spectra agree for dimers and trimers. Structures and spectral information for the trimer and the tetramer at density functional and MP2 level are provided. Selective self-aggregation and chiral recognition was observed for homochiral trimers. They exhibit a ring structure bound by OH...OH hydrogen bonds. A spectacular switch in the hydrogen bonding topology was observed for the tetramer. The homochiral enantiomer exhibits cooperative OH...OH bonding, while the heterochiral version shows isolated OH...O=C bonding in a symmetric SRSR arrangement. The crucial ingredients for this identification are the size-selective IR spectra with their different shifts and line patterns which are reproduced by the calculations.     

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.     

Cyclic Octamer of Hydroxyl-functionalized Cations with Net Charge Q=+8e Kinetically Stabilized by a ‘Molecular Island’ of Cooperative Hydrogen Bonds

Cyclic octamers are well-known structural motifs in chemistry, biology and physics. These include covalently bound cyclic octameric sulphur, cylic octa-alkanes, cyclo-octameric peptides as well as hydrogen-bonded ring clusters of alcohols. In this work, we show that even calculated cyclic octamers of hydroxy-functionalized pyridinium cations with a net charge Q=+8e are kinetically stable. Eight positively charged cations are kept together by hydrogen bonding despite the strong Coulomb repulsive forces. Sufficiently long hydroxy-octyl chains prevent “Coulomb explosion” by increasing the distance between the positive charges at the pyridinium rings, reducing the Coulomb repulsion and thus strengthen hydrogen bonds between the OH groups. The eightfold positively charged cyclic octamer shows spectroscopic properties similar to those obtained for hydrogen-bonded neutral cyclic octamers of methanol. Thus, the area of the hydrogen bonded OH ring represents a ‘molecular island’ within an overall cationic environment. Although not observable, the spectroscopic properties and the correlated NBO parameters of the calculated cationic octamer support the detection of smaller cationic clusters in ionic liquids, which we observed despite the competition with ion pairs wherein attractive Coulomb forces enhance hydrogen bonding between cation and anion.     

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.     

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.     

Investigations on mixed water-clusters: Gas phase titration with cyclopentanone and identification of some isomers by time-of-flight mass spectrometry

Mixed-clusters of water with cyclopentanone have been investigated using high resolution time-of-flight mass spectrometry. These clusters are synthesized in a gas-aggregation source at comparatively higher temperature. They contain water-cluster at the core and cyclopentanone molecules hydrogen bonded through ketone oxygen with the dangling OH available at the core. Thus these mixed-clusters may also be considered as the products of a titration in gas phase. The growth reaction reveals that all clusters are protonated. From the configuration of dimer and tetramer, it is suggested that the proton resides as an Eigen ion in the core. The protonated mixed-clusters containing six, seven and eight water molecules substantiate the hydronium contained hexa, hepta and octamer water-cluster structures predicted by [KJ(H₃O)⁺] model calculations. For clusters with 9–19 water molecules, the core appears to have configurations that give less than the predicted number of dangling bonds. In large size clusters having more than 20 water molecules, the water-core appears to have open configuration like the melted structures obtained as a result of increase in temperature.     

When Like Charged Ions Attract in Ionic Liquids: Controlling the Formation of Cationic Clusters by the Interaction Strength of the Counterions

The properties of ionic liquids are described by a subtle balance between Coulomb interaction, hydrogen bonding, and dispersion forces. We show that lowering the attractive Coulomb interaction by choosing weakly coordinating anions leads to the formation of cationic clusters. These clusters of like‐charged ions are stabilized by cooperative hydrogen bonding and controlled by the interaction potential of the anion. IR and NMR spectroscopy combined with computational methods are used to detect and characterize these unusual, counter‐intuitively formed clusters. They can be only observed for weakly coordinating anions. When cationic clusters are formed, cyclic tetramers are particularly stable. Therein, cooperative hydrogen‐bond attraction can compete with like‐charge repulsion. We present a simple but effective spectroscopic scale for the possibility of like‐charge attraction in ionic liquids, based on IR and NMR signatures.     

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.     

Structures and energetics of small lead cluster ions

By a combination of gas phase ion mobility measurements and relativistic density functional theory calculations with inclusion of spin-orbit coupling, we assign structures of lead cluster cations and anions in the range between 4 and 15 atoms. We find a planar rhombus for the tetramer, a trigonal bipyramid for the pentamer, and a pentagonal bipyramid for the heptamer, independent of charge state. For the hexamer, the cation and anion structures differ: we find an octahedron for the anion while the cation consists of fused tetrahedra. For the octamer, we find in both cases structures based on the pentagonal bipyramid motif plus adatom. For the larger clusters investigated we always find different structures for cations and anions. For example, Pb(12)(-) is confirmed to be a hollow icosahedron while Pb(12)(+) is a truncated filled icosahedron. Pb(13)(+) is a filled icosahedron but Pb(13)(-) is a hollow icosahedron with the additional atom capping a face. In order to get experimental information on the relative stabilities, we investigated the collision induced dissociation mass spectra for the different cluster sizes and charge states, and observe a strong correlation with the calculated fragmentation energies. Up to n = 13 the main fragmentation channel is atom loss; for the larger cluster sizes we observe fission into two large fragments. This channel is dominant for larger anions, less pronounced but clearly present for the cations.     

Molecular Mechanisms on the Selectivity Enhancement of Ascorbic Acid,Dopamine, and Uric Acid by Serine Oligomers Decoration on Graphene Oxide: A Molecular Dynamics Study

The selectivity in the simultaneous detection of ascorbic acid (AA), dopamine (DA), and uric acid (UA) has been an open problem in the biosensing field. Many surface modification methods were carried out for glassy carbon electrodes (GCE), including the use of graphene oxide and amino acids as a selective layer. In this work, molecular dynamics (MD) simulations were performed to investigate the role of serine oligomers on the selectivity of the AA, DA, and UA analytes. Our models consisted of a graphene oxide (GO) sheet under a solvent environment. Serine tetramers were added into the simulation box and were adsorbed on the GO surface. Then, the adsorption of each analyte on the mixed surface was monitored from MD trajectories. It was found that the adsorption of AA was preferred by serine oligomers due to the largest number of hydrogen-bond forming functional groups of AA, causing a 10-fold increase of hydrogen bonds by the tetraserine adsorption layer. UA was the least preferred due to its highest aromaticity. Finally, the role of hydrogen bonds on the electron transfer selectivity of biosensors was discussed with some previous studies. AA radicals received electrons from serine through hydrogen bonds that promoted oxidation reaction and caused the negative shifts and separation of the oxidation potential in experiments, as DA and UA were less affected by serine. Agreement of the in vitro and in silico results could lead to other in silico designs of selective layers to detect other types of analyte molecules.     

Infrared intensity in small ammonia and water clusters

Helium droplet technique has been used in order to measure the strength of the infrared absorption in small ammonia and water clusters as a function of size. Hydrogen bonding in ammonia and water dimers causes an enhancement of the intensity of the hydrogen stretching bands by a factor of four and three, respectively. Two types of the hydrogen bonded clusters show different size dependence of the infrared intensity per hydrogen bond. In ammonia (NH3)2 and (NH3)3 it is close to the crystal value. In water clusters, it increases monotonically with cluster size being in tetramers, a factor of two smaller than in the ice. The measured infrared intensity in water clusters is found to be a factor of two to three smaller as compared to the results of numerical calculations.     

Density Functional Theory Study of Water Diffusion and Clustering on Pd（111）

1 INTRODUCTION The interaction of water molecules with metal sur- faces plays a vital role in a number of important pro- cesses, such as corrosion, heterogeneous catalysis, electrochemical processes in aqueous solutions, hydrogen production, etc.[1] The structure and pro- perties of water adsorbed on well-defined metal sur- faces have been the subject of numerous experi- mental and theoretical investigations. There have been a number of experimental studies of water on metal surfaces throu…     

Enantiomeric β-sheet peptides from Aβ form homochiral pleated β-sheets rather than heterochiral rippled β-sheets

In 1953, Pauling and Corey postulated “rippled” β-sheets, composed of a mixture of d- and l-peptide strands, as a hypothetical alternative to the now well-established structures of “pleated” β-sheets, which they proposed as a component of all-l-proteins. Growing interest in rippled β-sheets over the past decade has led to the development of mixtures of d- and l-peptides for biomedical applications, and a theory has emerged that mixtures of enantiomeric β-sheet peptides prefer to co-assemble in a heterochiral fashion to form rippled β-sheets. Intrigued by conflicting reports that enantiomeric β-sheet peptides prefer to self-assemble in a homochiral fashion to form pleated β-sheets, we set out address this controversy using two β-sheet peptides derived from Aβ_17–23 and Aβ_30–36, peptides 1a and 1b. Each of these peptides self-assembles to form tetramers comprising sandwiches of β-sheet dimers in aqueous solution. Through solution-phase NMR spectroscopy, we characterize the different species formed when peptides 1a and 1b are mixed with their respective d-enantiomers, peptides ent-1a and ent-1b. ¹H NMR, DOSY, and ¹H,¹⁵N-HSQC experiments reveal that mixing peptides 1a and ent-1a results in the predominant formation of homochiral tetramers, with a smaller fraction of a new heterochiral tetramer, and mixing peptides 1b and ent-1b does not result in any detectable heterochiral assembly. ¹⁵N-edited NOESY reveals that the heterochiral tetramer formed by peptides 1a and ent-1a is composed of two homochiral dimers. Collectively, these NMR studies of Aβ-derived peptides provide compelling evidence that enantiomeric β-sheet peptides prefer to self-assemble in a homochiral fashion in aqueous solution.

In aqueous solution, mixtures of l- and d- macrocyclic β-sheet peptides derived from Aβ self-assemble to form homochiral pleated β-sheets but do not co-assemble to form heterochiral rippled β-sheets.