Locating protonated amines in clathrates

Uncovering the Pathway of Serine Octamer Magic Number Cluster Formation during Electrospray Ionization: Experiments and Simulations

Electrospray ionization (ESI) of serine (Ser) solution generates Ser8H+ as an abundant magic number cluster. ESI clustering of most other solutes yields nonspecific stoichiometries. It is unclear why Ser8H+ dominates in the case of Ser, and how Ser8H+ forms during ESI. Even the location of Ser8H+ formation is contentious (in solution, in ESI droplets, or elsewhere). Here we unravel key aspects of the l-Ser8H+ formation pathway. Harsh ion sampling conditions promote the collision-induced dissociation (CID) of regular ESI analytes. Unexpectedly, Ser8H+ was seemingly resistant against CID during ion sampling, despite its extremely low tandem mass spectrometry (MS/MS) stability. This unusual behavior reveals that Ser8H+ forms during ion sampling. We propose the following pathway: (1) Nonspecific Ser clusters are released when ESI droplets evaporate to dryness. These initial clusters cover a wide size range, from a few Ser to hundreds or thousands of monomers. (2) The clusters undergo dissociation during ion sampling, mostly via successive loss of neutral monomers. For any source activation voltage, there is a subpopulation of clusters for which this CID cascade tends to terminate at the octamer level, culminating in Ser8H+-dominated product distributions. Mobile proton molecular dynamics simulations were used to model the entire pathway. Ser8H+ structures formed in these simulations were consistent with ion mobility experiments. The most compact structures resembled the model of [Scutelnic, V. J. Am. Chem. Soc. 2018, 140, 7554-7560], with numerous intermolecular salt bridges and H-bonds. Our findings illustrate how the interplay of association and dissociation reactions across phase boundaries can culminate in magic number clusters.

Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids

Amide bond formation, the essential condensation reaction underlying peptide synthesis, is hindered in aqueous systems by the thermodynamic constraints associated with dehydration. This represents a key difficulty for the widely held view that prebiotic chemical evolution leading to the formation of the first biomolecules occurred in an oceanic environment. Recent evidence for the acceleration of chemical reactions at droplet interfaces led us to explore aqueous amino acid droplet chemistry. We report the formation of dipeptide isomer ions from free glycine or L-alanine at the air-water interface of aqueous microdroplets emanating from a single spray source (with or without applied potential) during their flight toward the inlet of a mass spectrometer. The proposed isomeric dipeptide ion is an oxazolidinone that takes fully covalent and ion-neutral complex forms. This structure is consistent with observed fragmentation patterns and its conversion to authentic dipeptide ions upon gentle collisions and for its formation from authentic dipeptides at ultra-low concentrations. It also rationalizes the results of droplet fusion experiments that show that the dipeptide isomer facilitates additional amide bond formation events, yielding authentic tri- through hexapeptides. We propose that the interface of aqueous microdroplets serves as a drying surface that shifts the equilibrium between free amino acids in favor of dehydration via stabilization of the dipeptide isomers. These findings offer a possible solution to the water paradox of biopolymer synthesis in prebiotic chemistry.

Manifolds of low energy structures for a magic number of hydrated sulfate: SO42-(H2O)24

Low energy structures of SO₄^2-(H₂O)₂₄ have been obtained using a combination of classical molecular dynamics simulations and refinement of structures and energies by quantum chemical calculations. Extensive exploration of the potential energy surface led to a number of low-energy structures, confirmed by accurate calibration calculations. An overall analysis of this large set was made after devising appropriate structural descriptors such as the numbers of cycles and their combinations. Low energy structures bear common motifs, the most prominent being fused cycles involving alternatively four and six water molecules. The latter adopt specific conformations which ensure the appropriate surface curvature to form a closed cage without dangling O-H bonds and at the same time provide 12-coordination of the sulfate ion. A prominent feature to take into account is isomerism via inversion of hydrogen bond orientations along cycles. This generates large families of ca. 100 isomers for this cluster size, spanning energy windows of 10-30 kJ mol^-1. This relatively ignored isomerism must be taken into account to identify reliably the lowest energy minima. The overall picture is that the magic number cluster SO₄^2-(H₂O)₂₄ does not correspond to formation of a single, remarkable structure, but rather to a manifold of structural families with similar stabilities. Extensive calculations on isomerization mechanisms within a family indicate that large barriers are associated to direct inversion of hydrogen bond networks. Possible implications of these results for magic number clusters of other anions are discussed.

Effects of Temperature on Cs+(H2O)20 Clathrate Structure

Clusters consisting of 20 water molecules and a single cesium ion are especially stable due to their clathrate structure that is composed exclusively of three-coordinate water molecules. Clathrate stability was investigated using infrared photodissociation (IRPD) spectroscopy in the free-OH stretching region (∼3600-3800 cm^-1) at ion cell temperatures between 135 and 355 K. At 275 K and colder, IRPD spectra of Cs⁺(H₂O)₂₀ have just one acceptor-acceptor-donor band. At higher temperatures, a higher-energy acceptor-donor band emerges and grows in intensity. Non-clathrate Na⁺(H₂O)₂₀ structures contain both of these bands, which do not change significantly in intensity over the temperature range. These results indicate a rapid onset in the conversion from clathrate to non-clathrate structures with temperature and suggest that some clathrate population remains even at the highest temperatures investigated. These results provide new insights into the role of entropy in clathrate stability.

Long distance ion-water interactions in aqueous sulfate nanodrops persist to ambient temperatures in the upper atmosphere

The effect of temperature on the patterning of water molecules located remotely from a single SO₄^2- ion in aqueous nanodrops was investigated for nanodrops containing between 30 and 55 water molecules using instrument temperatures between 135 and 360 K. Magic number clusters with 24, 36 and 39 water molecules persist at all temperatures. Infrared photodissociation spectroscopy between 3000 and 3800 cm^-1 was used to measure the appearance of water molecules that have a free O-H stretch at the nanodroplet surface and to infer information about the hydrogen bonding network of water in the nanodroplet. These data suggest that the hydrogen bonding network of water in nanodrops with 45 water molecules is highly ordered at 135 K and gradually becomes more amorphous with increasing temperature. An SO₄^2- dianion clearly affects the hydrogen bonding network of water to at least ∼0.71 nm at 135 K and ∼0.60 nm at 340 K, consistent with an entropic drive for reorientation of water molecules at the surface of warmer nanodrops. These distances represent remote interactions into at least a second solvation shell even with elevated instrumental temperatures. The results herein provide new insight into the extent to which ions can structurally perturb water molecules even at temperatures relevant to Earth's atmosphere, where remote interactions may assist in nucleation and propagation of nascent aerosols.

The effect of halide and iodate anions on the hydrogen-bonding network of water in aqueous nanodrops

The hydration of halide and iodate anions was investigated using electrospray ionization (ESI) mass spectrometry and infrared photodissociation (IRPD) spectroscopy.

A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates

Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

Effects of electronic structure on the hydration of PbNO3(+) and SrNO3(+) ion pairs

Hydration of PbNO3(+) and SrNO3(+) with up to 30 water molecules was investigated with infrared photodissociation (IRPD) spectroscopy and with theory. These ions are the same size, yet the IRPD spectra of these ion pairs for n = 2-8 are significantly different. Bands in the bonded O-H region (∼3000-3550 cm(-1)) indicate that the onset of a second hydration shell begins at n = 5 for PbNO3(+) and n = 6 for SrNO3(+). Spectra for [PbNO3](+)(H2O)2-5 and [SrNO3](+)(H2O)3-6 indicate that the structures of clusters with Pb(ii) are hemidirected with a void in the coordinate sphere. A natural bond orbital analysis of [PbNO3](+)(H2O)5 indicates that the anisotropic solvation of the ion is due to a region of asymmetric electron density on Pb(ii) that can be explained by charge transfer from the nitrate and water ligands into unoccupied p-orbitals on Pb(ii). There are differences in the IRPD spectra of PbNO3(+) and SrNO3(+) with up to 25 water molecules attached. IR intensity in the bonded O-H region is blue-shifted by ∼50 cm(-1) in nanodrops containing SrNO3(+) compared to those containing PbNO3(+), indicative of a greater perturbation of the water H-bond network by strontium. The free O-H stretches of surface water molecules in nanodrops containing 10, 15, 20, and 25 water molecules are red-shifted by ∼3-8 cm(-1) for PbNO3(+) compared to those for SrNO3(+), consistent with more charge transfer between water molecules and Pb(ii). These results demonstrate that the different electronic structure of these ions significantly influences how they are solvated.

Hydration of guanidinium depends on its local environment

Hydration of gaseous guanidinium (Gdm+) with up to 100 water molecules attached was investigated using infrared photodissociation spectroscopy in the hydrogen stretch region between 2900 and 3800 cm-1. Comparisons to IR spectra of low-energy computed structures indicate that at small cluster size, water interacts strongly with Gdm+ with three inner shell water molecules each accepting two hydrogen bonds from adjacent NH2 groups in Gdm+. Comparisons to results for tetramethylammonium (TMA+) and Na+ enable structural information for larger clusters to be obtained. The similarity in the bonded OH region for Gdm(H2O)20+vs. Gdm(H2O)100+ and the similarity in the bonded OH regions between Gdm+ and TMA+ but not Na+ for clusters with <50 water molecules indicate that Gdm+ does not significantly affect the hydrogen-bonding network of water molecules at large size. These results indicate that the hydration around Gdm+ changes for clusters with more than about eight water molecules to one in which inner shell water molecules only accept a single H-bond from Gdm+. More effective H-bonding drives this change in inner-shell water molecule binding to other water molecules. These results show that hydration of Gdm+ depends on its local environment, and that Gdm+ will interact with water even more strongly in an environment where water is partially excluded, such as the surface of a protein. This enhanced hydration in a limited solvation environment may provide new insights into the effectiveness of Gdm+ as a protein denaturant.

Diphenylalanine self assembly: novel ion mobility methods showing the essential role of water

The mechanism and driving forces behind the formation of diphenylalanine (FF) nanotubes have attracted much attention in the past decades. The hollow structure of the nanotubes suggests a role for water during the self-assembly process. Here, we use novel ion-mobility mass spectrometry methods to probe the early oligomers formed by diphenylalanine peptides. Interestingly, water-bound oligomers are observed in nano-electrospray ionization (ESI) mass spectra in the absence of bulk solvent. In addition, ligated water clusters transit the ion mobility cell but (often) dissociate before detection. These water molecules are shown to be essential for the formation of diphenylalanine oligomers larger than the dimer. The ligated water molecules exist in the solvent free environment either as neutral water or as protonated water clusters, depending on the composition of solvent from which they are sprayed. Water adduction helps stabilize conformers that are otherwise energetically unstable ultimately leading to the assembly of FF nanotubes.

Upregulation of BMSCs osteogenesis by positively-charged tertiary amines on polymeric implants via charge/iNOS signaling pathway

Positively-charged surfaces on implants have a similar potential to upregulate osteogenesis of bone marrow-derived mesenchymal stem cells (BMSCs) as electromagnetic therapy approved for bone regeneration. Generally, their osteogenesis functions are generally considered to stem from the charge-induced adhesion of extracellular matrix (ECM) proteins without exploring the underlying surface charge/cell signaling molecule pathways. Herein, a positively-charged surface with controllable tertiary amines is produced on a polymer implant by plasma surface modification. In addition to inhibiting the TNF-α expression, the positively-charged surface with tertiary amines exhibits excellent cytocompatibility as well as remarkably upregulated osteogenesis-related gene/protein expressions and calcification of the contacted BMSCs. Stimulated by the charged surface, these BMSCs display high iNOS expressions among the three NOS isoforms. Meanwhile, downregulation of the iNOS by L-Can or siRNA inhibit osteogenic differentiation in the BMSCs. These findings suggest that a positively-charged surface with tertiary amines induces osteogenesis of BMSCs via the surface charge/iNOS signaling pathway in addition to elevated ECM protein adhesion. Therefore, creating a positively-charged surface with tertiary amines is a promising approach to promote osseointegration with bone tissues.

An infrared spectroscopic and theoretical study on (CH3)3N–H+–(H2O)n, n = 1–22: highly polarized hydrogen bond networks of hydrated clusters

Highly polarized water networks are found in the micro hydaration of protonated trimethylamine.

Evolution of Hydrogen-Bond Networks in Protonated Water Clusters H(+)(H2O)n (n = 1 to 120) Studied by Cryogenic Ion Mobility-Mass Spectrometry

Cryogenic (80 K) ion mobility-mass spectrometry (cryo-IM-MS) is employed to study structural transitions of protonated water clusters in both the small, H(+)(H2O)n (n = 1 to 30), and large, (n = 31 to ∼120), size regions. In agreement with previous studies, we find compelling evidence of regions of uniform cluster decay in the small size region, accompanied by sharp transition points whereby the loss of a single water monomer induces a different H-bonding motif. The investigation of the isomeric distribution of each species at 80 K reveals experimental evidence supporting the notion that H(+)(H2O)n (n = 6) is the smallest system to possess both Eigen- (H3O(+)) and Zundel- (H5O2(+)) centered structures. Cryo-IM-MS is particularly well-suited for studying clusters in the large size region, for which previous spectroscopic experimental studies are scarce.