The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods

The impact of side-chain fluorination on proton-bound phenylalanine dimers: a cryogenic infrared spectroscopic study

The incorporation of fluorine into amino acids is an important strategy to produce tailored building blocks with unique properties for peptide-based materials. Phenylalanine is frequently modified due to its role in cation-π interactions and the formation of amyloid fibres. Previous studies have utilized gas-phase vibrational spectroscopy to study interactions between canonical amino acids. In this study, we employ a combination of cryogenic gas-phase infrared spectroscopy and density functional theory to study the interactions in proton-bound dimers of side-chain fluorinated phenylalanines. Our findings reveal how the position and number of fluorine atoms affect the interactions and structures of the dimers. Monofluorinated phenylalanines adopt charge-solvated structures in which the two amino acids interact via their ammonium and amine functions (NH3+⋯NH2). The dimer with the perfluorinated side chain forms multiple charge-solvated and salt-bridged structures with varying interaction types. These structural changes are attributed to the significant reduction of electron density in the aromatic systems.

Indication of 310-Helix Structure in Gas-Phase Neutral Pentaalanine

We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm^-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 3₁₀-helix with two β-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.

IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase

We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm-1. Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.

Gas-Phase Structural Analysis of Supramolecular Assemblies

Ion mobility spectrometry and gas-phase IR action spectroscopy are two structure-sensitive mass-spectrometric methods becoming more popular recently. While ion mobility spectrometry provides collision cross sections as a size and shape dependent parameter of an ion of interest, gas-phase spectroscopy identifies functional groups and is capable of distinguishing different isomers. Both methods have recently found application for the investigation of supramolecular assemblies. We here highlight several aspects.Starting with the characterization of switching states in azobenzene photoswitches as well as redox-switchable lasso-type pseudorotaxanes, structures of isomers can be distinguished and mechanistic details analyzed. Ion mobility mass spectrometry in combination with gas-phase H/D-exchange reactions unravels subtle structural details as described for the chiral recognition of crown ether amino acid complexes. Gas-phase IR spectroscopy allows identification of details of the binding patterns in dimeric amino acid clusters as well as the serine octamer. This research can be extended into the analysis of peptide assemblies that are of medical relevance, for example, in Alzheimer's disease, and into a general hydrophobicity scale for natural as well as synthetic amino acids. The development of ultracold gas-phase spectroscopy that for example makes use of ions trapped in liquid helium droplets provides access to very well resolved spectra. The combination of ion mobility separation of ions with subsequent spectroscopic analysis even permits separation of different isomers and studying them separately with respect to their structure. This represents a great advantage of these gas-phase methods over solution experiments, in which the supramolecular complexes under study typically equilibrate and thus prevent a separate investigation of different isomers. At the end of this overview, we will discuss larger and more complex supramolecules, among them giant halogen-bonded cages and complex intertwined topologies such as molecular knots and Solomon links.

Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay

The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]⁺ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]⁺ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm^-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.

Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations

The structures of three proton-bound dimers (Met₂H⁺, MetTrpH⁺, and Trp₂H⁺) are investigated in the gas phase with infrared multiple photon disassociation (IRMPD) spectroscopy in combination with quantum chemical calculations. Their IRMPD spectra in the range of 600–1850 cm^–1 are obtained experimentally using an FT-ICR mass spectrometer and the CLIO free electron laser as an IR light source. The most abundant conformers are elucidated by comparing the IRMPD spectra with harmonic frequencies obtained at the B3LYP-GD3BJ/6-311++G** level of theory. Discrepancies between the experimental and theoretical data in the region of 1500–1700 cm^–1 are attributed to the anharmonicity of the amino bending modes. We confirm the result of a previous IRMPD study that the structure of gas-phase Trp₂H⁺ is charge-solvated but find that there are more stable structures than originally reported (Feng, R.; Yin, H.; Kong, X. Rapid Commun. Mass Spectrom.2016, 30, 24–28). In addition, gas-phase Met₂H⁺ and MetTrpH⁺ have been revealed to have charge-solvated structures. For all three dimers, the most stable conformer is found to be of type A. The spectrum of Met₂H⁺, however, cannot be explained without some abundance of type B charge-solvated conformers as well as salt-bridged structures.

Strong intramolecular hydrogen bonding in protonated β-methylaminoalanine: A vibrational spectroscopic and computational study

The gas-phase structure of protonated β-methylaminoalanine was investigated using infrared multiple photon dissociation spectroscopy in the C-H, N-H, O-H stretching region (2700-3800 cm^-1) and the fingerprint region (1000-1900 cm^-1). Calculations using density functional theory methods show that the lowest energy structures prefer protonation of the secondary amine. Formation of hydrogen bonds between the primary and secondary amine, and the secondary amine and carboxylic oxygen further stabilize the lowest energy structure. The infrared spectrum of the lowest energy structure originating with harmonic density functional theory has features that generally match the positions of the experimental spectra; however, the overall agreement with the experimental spectrum is poor. Molecular dynamics calculations were used to generate a gas-phase infrared spectrum. With these calculations a reasonable match with the experimental spectrum, especially in the high-energy region, was obtained. The results of the molecular dynamics simulation support the density functional theory calculations, with protonation of the secondary amine and the formation of a hydrogen bond between the protonated secondary amine and the primary amine. This work shows the importance of accounting for anharmonic effects in systems with very strong intramolecular hydrogen bonding.

Research on the Effects of Drying Temperature on Nitrogen Detection of Different Soil Types by Near Infrared Sensors

Soil is a complicated system whose components and mechanisms are complex and difficult to be fully excavated and comprehended. Nitrogen is the key parameter supporting plant growth and development, and is the material basis of plant growth as well. An accurate grasp of soil nitrogen information is the premise of scientific fertilization in precision agriculture, where near infrared sensors are widely used for rapid detection of nutrients in soil. However, soil texture, soil moisture content and drying temperature all affect soil nitrogen detection using near infrared sensors. In order to investigate the effects of drying temperature on the nitrogen detection in black soil, loess and calcium soil, three kinds of soils were detected by near infrared sensors after 25 °C placement (ambient temperature), 50 °C drying (medium temperature), 80 °C drying (medium-high temperature) and 95 °C drying (high temperature). The successive projections algorithm based on multiple linear regression (SPA-MLR), partial least squares (PLS) and competitive adaptive reweighted squares (CARS) were used to model and analyze the spectral information of different soil types. The predictive abilities were assessed using the prediction correlation coefficients (R_P), the root mean squared error of prediction (RMSEP), and the residual predictive deviation (RPD). The results showed that the loess (R_P = 0.9721, RMSEP = 0.067 g/kg, RPD = 4.34) and calcium soil (R_P = 0.9588, RMSEP = 0.094 g/kg, RPD = 3.89) obtained the best prediction accuracy after 95 °C drying. The detection results of black soil (R_P = 0.9486, RMSEP = 0.22 g/kg, RPD = 2.82) after 80 °C drying were the optimum. In conclusion, drying temperature does have an obvious influence on the detection of soil nitrogen by near infrared sensors, and the suitable drying temperature for different soil types was of great significance in enhancing the detection accuracy.

Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers

The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm⁻¹ and theory.

Influence of Linkage Stereochemistry and Protecting Groups on Glycosidic Bond Stability of Sodium Cationized Glycosyl Phosphates

Energy-resolved collision-induced dissociation (ER-CID) experiments of sodium cationized glycosyl phosphate complexes, [GP _x +Na]⁺, are performed to elucidate the effects of linkage stereochemistry (α versus β), the geometry of the leaving groups (1,2-cis versus 1,2-trans), and protecting groups (cyclic versus non-cyclic) on the stability of the glycosyl phosphate linkage via survival yield analyses. A four parameter logistic dynamic fitting model is used to determine CID_50% values, which correspond to the level of rf excitation required to produce 50% dissociation of the precursor ion complexes. Present results suggest that dissociation of 1,2-trans [GP _x +Na]⁺ occurs via a McLafferty-type rearrangement that is facilitated by a syn orientation of the leaving groups, whereas dissociation of 1,2-cis [GP_x+Na]⁺ is more energetic as it involves the formation of an oxocarbenium ion intermediate. Thus, the C1-C2 configuration plays a major role in determining the stability/reactivity of glycosyl phosphate stereoisomers. For 1,2-cis anomers, the cyclic protecting groups at the C4 and C6 positions stabilize the glycosidic bond, whereas for 1,2-trans anomers, the cyclic protecting groups at the C4 and C6 positions tend to activate the glycosidic bond. The C3 O-benzyl (3 BnO) substituent is key to determining whether the sugar or phosphate moiety retains the sodium cation upon CID. For 1,2-cis anomers, the 3 BnO substituent weakens the glycosidic bond, whereas for 1,2-trans anomers, the 3 BnO substituent stabilizes the glycosidic bond. The C2 O-benzyl substituent does not significantly impact the glycosidic bond stability regardless of its orientation. Graphical abstract ᅟ.

Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline

Strongly hydrated l-proline cooperatively binds Na⁺ and Cl⁻ ions in aqueous solution.

Structures and unimolecular chemistry of M(Pro2-H)+(M = Mg, Ca, Sr, Ba, Mn, Fe, Co, Ni, Cu, Zn) by IRMPD spectroscopy, SORI-CID, and theoretical studies

M(Pro₂-H)⁺complexes were electrosprayed and isolated in an FTICR cell where their unimolecular chemistries and structures were explored using SORI-CID and IRMPD spectroscopy.