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The conformations of the unsolvated dimers and trimers produced by electrospraying mixtures of polyalanine-based peptides have been examined using ion mobility measurements in conjunction with molecular dynamics simulations. These multimers can provide models for how the secondary structure associates into the motifs that makeup the tertiary structure domains of proteins. Mixtures of helix-forming monomers (Ac−A14K and Ac−A15K and Ac−(GA)7K and Ac−A(GA)7K; Ac = acetyl, G = glycine, A = alanine, and K = lysine) yield V-shaped helical dimers where the C termini are tethered together by the protonated lysine side chain from one peptide interacting with the C terminus of the other (exchanged lysines). Trimers from the Ac−(GA)7K and Ac−A(GA)7K mixture adopt a pinwheel arrangement of helices with all three C termini tethered together by exchanged lysines. Trimers are much less abundant for the Ac−A14K and Ac−A15K mixture. The V-shaped dimer and pinwheel trimer arrangement leads to a cooperative electrostatic stabilization of the helices through the interaction of the combined charge with the helix dipoles. Mixtures of globule-forming monomers (Ac−K(GA)7 and Ac−KA(GA)7) form predominantly globular multimers. In some conformations, however, the helical state is stabilized by interactions with the local environment. Examples include the antiparallel arrangement of helices that is present as a minor component for the Ac−K(GA)7·Ac−KA(GA)7+2H⁺ dimer and dominant for the Ac−KA14·Ac−KA15+2H⁺ dimer, as well as conformations with one or more helices which occur for the trimers from the Ac−K(GA)7 and Ac−KA(GA)7 mixture.

Electrospray ionization sampling of 0.01 M solutions of serine reveals an unusually abundant protonated serine octamer, which demonstrates a strong preference for homochirality. Ion mobility spectra yield an experimental cross section that is consistent with a single “cubic” structure. Density functional theory calculations support experimental observations which suggest that the structure of the serine octamer is closely related to and formed from a small subsection of the crystal structure of anhydrous serine. The formation, bonding, and experimental constraints placed on the serine octamer are discussed in light of the proposed nanocrystalline structure. The mass spectra of the analogous molecules threonine and homoserine exhibit several similar features with that of serine and the likely structures for the octameric species are compared with that of the serine octamer. Finally, implications for the spontaneous symmetry breaking of a racemic mixture and the origin of life are addressed.

A novel laser photolysis source has been used to synthesize hydrogen-terminated silicon clusters SinHx⁺, where n ≤ 50. Using mass spectrometry, the hydrogen content of the SinHx⁺ clusters with n = 10−30 was measured as a function of temperature from 300 to 950 K. For n = 10−22 at the lower temperatures, there is a broad distribution of [H]/[Si] ratios which peak around compositions expected for clusters with bulklike silicon cores (x/n > 1). SinHx⁺ clusters with x/n ≅ 1 appear to be favored at intermediate temperatures. This stoichiometric composition suggests three-dimensional, SinHn⁺ cage-like structures built from Si−H units. The stability of the cage geometries is supported by density functional calculations. For cluster cations with n ≥ 23 an abrupt transition occurs and there is a sharp drop in the hydrogen content at the lower temperatures. For these clusters, SinH(n-y)⁺ (y = 1−5) compositions are prominent at the higher temperatures. These compositions suggest cage-like geometries with one or more internal silicon atoms. By adjusting the source conditions it is possible to generate SinHx⁺ (n ≥ 23) clusters with a narrow distribution of x (less than two hydrogens wide).

Protonated polyalanine peptides form helices in the gas phase when their most basic protonation site (the N-terminus) is blocked by acetylation:  Ac-An+H⁺ (Ac = acetyl and A = alanine). The glycine analogues, Ac-Gn+H⁺ (G = glycine), on the other hand, form random globules. The disruption of helix formation in unsolvated Ac-AnGxAm+H⁺ peptides has been examined as a function of n+m, and x using high resolution ion mobility measurements and molecular dynamics simulations. A surprisingly large block of glycine residues is required to disrupt helix formation in these peptides. For example, Ac-A5G3A5+H⁺ and Ac-A6G5A6+H⁺ both remain helical at room temperature. According to molecular dynamics simulations, the glycines do not cause a localized disruption of the helices, as might be expected for a residue considered a helix breaker. This is consistent with helix disruption occurring through a global effect on the relative energies of the helix and globule rather than through a localized entropic effect.

The surface plasmon polariton-enhanced Raman spectra of size-selected, matrix-isolated C14 neutral clusters are presented along with the calculated vibrational frequencies for the ring and linear chain isomers. The Raman spectra show resonance enhancement over a range of excitation wavelengths from 457.9 to 514.5 nm. The measured vibrational spectra are most consistent with the linear chain isomer. In addition, fluorescence spectra of neutral, mass-selected Cn (n = 14 and 18) clusters are presented. The isolated C14 clusters display strong fluorescence with vibrational structure between 520 and 700 nm. The origins of the observed fluorescence for both C14 and C18 are investigated using the ZINDO/S, CIS, and TD-B3LYP methods.

The conformations of unsolvated glycine-based peptides have been probed using high-resolution ion mobility measurements and molecular dynamics simulations. Alanine-based Ac-Alan-LysH⁺ peptides have previously been shown to form helices in the gas phase. In contrast, the polyglycine analogues (Ac-Glyn-LysH⁺) do not form helices at room temperature; they adopt random globular conformations. Thus, the stabilities of alanine and glycine helices in vacuo are consistent with the helix propensities in aqueous solution, where alanine has the highest helix propensity and glycine has one of the lowest.