Spectroscopic evidence for gas-phase formation of successive beta-turns in a three-residue peptide chain

We report the first gas-phase spectroscopic study of a three-residue model of a peptide chain, Ac-Phe-Gly-Gly-NH2 (Ac = acetyl), using the IR/UV double resonance technique. The existence of at least five different conformers under supersonic expansion conditions is established, most of them exhibiting rather strong intramolecular H-bonds. One of the most populated conformers, however, exhibits a different H-bonding network characterized by two weak H-bonds. Comparison of the amide A and I/II experimental data with density functional theory calculations carried out on a series of selected conformations enables us to assign this conformer to two successive beta-turns along the peptide chain, the two H-bonds being of C10 type, i.e., each of them closing a 10-atom ring in the molecule. The corresponding form is found to be more stable than the 310 helix secondary structure (not observed), presumably because of specific effects due to the glycine residues.     

Spectroscopic evidence for the formation of helical structures in gas-phase short peptide chains

Aminoisobutyric acid (Aib) is a synthetic amino acid known to favor the formation of 3(10) helical structures in condensed phases, namely, crystals. The intrinsic character of these helicogenic properties has been investigated on the Ac-Aib-Phe-Aib-NH2 molecule under isolated conditions, namely, in the gas phase, both experimentally by double-resonance IR/UV spectroscopy and theoretically by quantum chemistry. A convergent set of evidence, based on energetic, IR, and UV spectroscopic data as well as on analogies with the similar peptide Ac-Ala-Phe-Ala-NH2 previously studied, enables us to conclude the formation of an incipient 310 helix in these isolated systems.     

Intrinsic acidity of dimethylhalonium ions: evidence for hyperconjugation in dimethylhalonium ylides in the gas phase

The intrinsic acidity of dimethylhalonium ions has been determined, both by theoretical methods and by gas-phase reactions of the isolated ions with pyridine bases. The calculated geometry of the dimethylhalonium ions shows a bent structure with the C-X-C angle decreasing in the order Cl > Br > I. Thermochemical calculations for the reaction of the dimethylhalonium ions with pyridine, 2,6-dimethylpyridine, and 2,6-di-tert-butylpyridine indicate that proton transfer, with the formation of the dimethylhalonium ylide is endothermic, whereas methyl transfer, with formation of methylhalide, is exothermic. The endothermicities for proton transfer are, nevertheless, dependent on the steric hindrance of the base. The bulkier the bases, the less endothermic the proton-transfer reaction is. Experimental gas-phase reactions support the calculations, showing that methyl transfer is the major reaction of dimethylchloronium and dimethyliodonium with pyridine, whereas proton transfer, as well as single electron transfer, is observed for the bulkier bases. The calculations also indicate that acidity increases in the order chloronium > bromonium > iodonium. NBO calculations predict that hyperconjugation with the sigma carbon-halogen orbital plays a role in stabilizing the halonium ylide species in the gas phase.     

Controlled formation of peptide bonds in the gas phase

Photoexcitation (using 157 nm vacuum ultraviolet radiation) of proton-bound peptide complexes leads to water elimination and the formation of longer amino acid chains. Thus, it appears that proton-bound dimers are long-lived intermediates along the pathway to peptide formation. Product specificity can be controlled by selection of specific complexes and the incorporation of blocking groups at the N- or C-termini. The product peptide sequences are confirmed using collision-induced dissociation.     

Secondary structures of short peptide chains in the gas phase: double resonance spectroscopy of protected dipeptides

The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH(2), Xxx=Gly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH(2) permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly gamma-fold corresponding to the 2(7) ribbon structure. Topologically, this motif is very close to a beta-strand backbone conformation. The second conformation observed is the beta-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the beta-turn structure, even in the absence of a solvent. The beta-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH(2) peptide, with its two bulky side chains, exhibits the largest beta-turn population. This suggests that the intrinsic stabilities of the 2(7) ribbon and the beta-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.     

Rate and extent of gas-phase hydrogen/deuterium exchange of bradykinins: evidence for peptide zwitterions in the gas phase

The gas-phase H/D exchange of bradykinin [M + H]⁺, [M + Na]⁺, [M + 2H]²⁺, and [M + H + Na]²⁺ ions; des-Arg¹-bradykinin, des-Arg⁹-bradykinin, and bradykinin fragment 2-7 [M + H]⁺ ions; and O-methylbradykinin [M + H]⁺ and [M + 2H]²⁺ ions with D₂O have been examined by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry at 9.4 T. The different peptides vary widely in exchange rate and extent of deuterium incorporation. H/D exchange was slowest and deuterium incorporation was least for bradykinin [M + H]⁺, [M + H + Na]²⁺ and bradykinin methyl ester [M + 2H]²⁺ ions. In contrast, H/D exchange and extent of deuteration are higher for des-Arg¹-bradykinin, des-Arg⁹-bradykinin, and bradykinin fragment 2-7 [M + H]⁺ ions; and highest for bradykinin [M + Na]⁺ and [M + 2H]²⁺, and O-methylbradykinin [M + H]⁺. Because the most likely site of protonation is the guanidino group of arginine, the above reactivity pattern strongly supports a zwitterion form for protonated gas-phase bradykinin.     

Uncatalyzed peptide bond formation between two double amino acid molecules in the gas phase

The gas phase mechanism for peptide bond formation between two double amino acid (DAA) molecules ((NH₂)₂C(COOH)₂) is investigated in the absence of any catalysts. Two different paths, concerted and stepwise, each leading to both cis and trans DAA‐DAA dipeptide products (four mechanisms total) are examined on the basis of theoretical calculations carried out at the CCSD(T)/aug‐cc‐pVDZ//MP2/aug‐cc‐pVDZ level. The investigation indicates that the concerted mechanism leading to the trans configuration of the peptide bond in the DAA‐DAA dipeptide product is thermodynamically favored by about 5 kcal mol^?1 and requires slightly less energy than the remaining pathways considered. Moreover, the peptide bond formation process between two DAA molecules in the gas phase resembles the analogous reactions between two natural amino acids.     

Solid phase insertion of diamines into peptide chains

Diamines derived from naturally occurring aminoacids were inserted into peptide chains by the reaction of the monophthaloyl diamines with amino acid 1-benzotriazolyl esters, bound through their amino functions onto trityl-type resins. The phthaloyl group was removed and peptide chains using N-Fmoc amino acids, were assembled on the liberated amino function. The peptidyl diamides obtained, were cleaved from the resins with ^tBu-side chain protection remaining intact, or fully deprotected.     

Heat of formation for sec-butyl cation in the gas phase

The ionization energies and [C₄H₉]⁺ appearance energies for several 2-substituted butanes have been measured by photoionization mass spectrometry. Using the stationary electron convention, a 298 K heat of formation of 771±3 kJ mol^?1 is derived for the sec-butyl cation in the gas phase. A value of 747±3 kJ mol^?1 is calculated for the proton affinity of trans-2-butene.     

Interaction of gas phase atomic hydrogen with Pt(111):Direct evidence for the formation of bulk hydrogen species

Employing hot tungsten filament to thermal dissociate molecular hydrogen,we generated gas phase atomic hydrogen under ultra-high vacuum(UHV)conditions and investigated its interaction with Pt(111) surface.Thermal desorption spectroscopy(TDS)results demonstrate that adsorption of molecular hy- drogen on Pt(111)forms surface Had species whereas adsorption of atomic hydrogen forms not only surface Had species but also bulk Had species.Bulk Had species is more thermal-unstable than surface Had species on Pt(111),suggesting that bulk Had species is more energetic.This kind of weakly- adsorbed bulk Had species might be the active hydrogen species in the Pt-catalyzed hydrogenation reactions.     

Complete infrared spectroscopic characterization of phenol-borane-trimethylamine dihydrogen-bonded complex in the gas phase

In the paper we report the first observation of the vibrational spectrum in the B-H stretching region in the gas phase for a dihydrogen bonded complex. The appearance of three transitions for the B-H stretching modes of a (di)hydrogen-bonded complex involving borane-trimethylamine indicates the lowering of the symmetry on the BH3 group upon interaction with phenol. Further, the shift in the O-H stretching frequency indicates that phenol is hydrogen bonded to borane-trimethylamine. The two sets of the present data establish, unequivocally, the formation of O-H...H-B dihydrogen-bonded complex between phenol and borane-trimethylamine.     

Relay stations for electron hole migration in peptides: possibility for formation of three-electron bonds along peptide chains

Our calculations found that the O thereforeO three-electron (3e) bonds (2.16 approximately 2.27 A) can be formed not only between two neighboring peptide units in a main chain but also between two adjacent peptide units in two different main chains in proteins. This finding may address electron hole migration from one peptide unit to the next in proteins. Evidently, stability of the O thereforeO 3e bonded species is strongly dependent on the component of the oligopeptides and is reduced owing to the steric hindrance of the side chains when the big chains present in oligopeptides. Besides, formation of the O thereforeO 3e bonds competes with the formation of the other forms of three-electron bonds depending on the component of the polypeptides. Formation of the O thereforeS 3e bond is thermodynamically more favorable than that of the O thereforeO 3e bond for the oligopeptides containing sulfur atom in their side chains. Similarly, formation of the O thereforepi 3e bond between aromatic ring of the side chain and the neighboring peptide unit is more stable than that of the O thereforeO 3e bond when the aromatic amino acids present in the oligopeptides. We infer that a series of three-electron bonds may be formed during the electron hole migration along the peptide backbone in proteins and assist electron hole transport as relay stations, supporting the peptide chain as a conduction wire. The ab initio molecular dynamics simulations of the polypeptides also support this conclusion.     

Valence anions of N-acetylproline in the gas phase: computational and anion photoelectron spectroscopic studies

We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)(-), measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP∕6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.     

A kinetic model for formation of nanodisperse matter in the gas phase

Taking CsI aerosol as an example, it was shown that growth of primary aerosol particles can be described in terms of both discrete and continuum models. This conclusion is based on the results of experiments carried out using a method that makes it possible to distinguish primary particles against the background of their aggregates, to provide a complete transfer of the primary particles from aerosol bulk to a collector, and to determine the particle sizes by transmission electron microscopy. Under the conditions studied, the size distribution of the primary particles is described by a Fokker—Planck type equation.     

Light-activated hydrogel formation via the triggered folding and self-assembly of a designed peptide

Photopolymerization can be used to construct materials with precise temporal and spatial resolution. Applications such as tissue engineering, drug delivery, the fabrication of microfluidic devices and the preparation of high-density cell arrays employ hydrogel materials that are often prepared by this technique. Current photopolymerization strategies used to prepare hydrogels employ photoinitiators, many of which are cytotoxic and require large macromolecular precursors that need to be functionalized with moieties capable of undergoing radical cross-linking reactions. We have developed a simple light-activated hydrogelation system that employs a designed peptide whose ability to self-assemble into hydrogel material is dependent on its intramolecular folded conformational state. An iterative design strategy afforded MAX7CNB, a photocaged peptide that, when dissolved in aqueous medium, remains unfolded and unable to self-assemble; a 2 wt % solution of freely soluble unfolded peptide is stable to ambient light and has the viscosity of water. Irradiation of the solution (260 < lambda < 360 nm) releases the photocage and triggers peptide folding to produce amphiphilic beta-hairpins that self-assemble into viscoelastic hydrogel material. Circular dichroic (CD) spectroscopy supports this folding and self-assembly mechanism, and oscillatory rheology shows that the resulting hydrogel is mechanically rigid (G' = 1000 Pa). Laser scanning confocal microscopy imaging of NIH 3T3 fibroblasts seeded onto the gel indicates that the gel surface is noncytotoxic, conducive to cell adhesion, and allows cell migration. Lastly, thymidine incorporation assays show that cells seeded onto decaged hydrogel proliferate at a rate equivalent to cells seeded onto a tissue culture-treated polystyrene control surface.     

UV resonance Raman spectroscopic monitoring of supramolecular complex formation: peptide recognition in aqueous solution

The formation of a supramolecular complex between a tetrapeptide and an artificial receptor , is monitored at submillimolar concentrations in water by UV resonance Raman spectroscopy. Using 275 nm excitation, we selectively probe the carboxylate binding site (CBS) within the receptor, a moiety which is very efficient in binding the carboxy terminus of peptides in aqueous media. Complexation of the receptor with the tetrapeptide involves the formation of a H-bond enforced ion pair, resulting in significant changes in the corresponding UV resonance Raman spectra. Our qualitative interpretation is based on experimental reference and calculated Raman spectra on model systems. First preliminary calculations show that for a quantitative analysis, also the distinct contributions of multiple CBS conformers must be considered in addition to the H-bond induced changes upon complexation.     

Cyclic peptide as reference system for b ion structural analysis in the gas phase

Infrared multiple photon dissociation spectroscopy and hydrogen/deuterium exchange methods are used to confirm the macrocylic structure of a b(6) peptide fragment by direct comparison with a synthetically made cyclic peptide. The acetylation of the peptide N-terminus results in the inhibition of the macrocyclic formation, supporting the "head-to-tail" cyclization mechanism. Differences in hydrogen/deuterium exchange rates for macrocyclic and oxazalone structure peptide fragments are interpreted to be a result of the complex interplay of multiple basic sites in the peptide fragment, supporting the relay mechanism for deuterium exchange with CH(3)OD.     

Infrared and mass spectroscopic evidence for hydrocarbon formation on a supported cobalt catalyst

Interrupting the surface carbonyl development at 345 K on an aerosilsupported cobalt oxide catalyst in CO/H₂ atmosphere at maximum surface concentration of linear carbonyl species by heating to 475 K results in the formation of Fischer-Tropsch type products detectable by combined IR and MS measurements.

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345°K , , CO/H₂ , 475° -, .

     

Applications of chemometric methods to spectroscopic studies of aggregate formation and twisted intramolecular charge transfer in the gas phase and in non-polar solvents

Principal component analysis—self-modelling and non-linear least-squares spectral resolution methods were applied to quantitative fluorescence studies of the aggregate formation and the twisted intramolecular charge transfer (TICT) state emission of p-(N,N-diethylamino)ethylbenzoate (DEAEB) in the gas phase and in low-density supercritical ethane. A broad Gaussian-like fluorescence band at approximately 400 nm was obtained and assigned to the emission of DEAEB microcrystals or microsolids. It is shown that the red-shifted band can essentially be eliminated by keeping the sample undisturbed for a period of time and by selecting appropriate excitation wavelengths. The results support the conclusion that even in the gas phase the contribution of DEAEB TICT state emission is still significant. It is also demonstrated that a quantitative characterization of the excited state equilibium between the locality excited and TICT states of DEAEB in non-polar solvents can be accomplished by application of a spectral resolution method.