Mid- and Near-Infrared Spectra of Conformers of H-Pro-Trp-OH

Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures

Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT. We provide a benchmark of several computational methods (GAFF, AMOEBApro13, PM6, PM7, DFTB3-D3(BJ)) as possible prescanning surrogates and apply sGADFT to two test case systems that are (i) two isomer families of the protonated Gly-Pro-Gly-Gly tetrapeptide (Masson, A.; J. Am. Soc. Mass Spectrom.2015, 26, 1444-1454) and (ii) the doubly protonated cyclic decapeptide gramicidin S (Nagornova, N. S.; J. Am. Chem. Soc.2010, 132, 4040-4041). We show that our GA procedure can correctly identify low-energy minima in as little as a few hours. Subsequent refinement of surrogate low-energy structures within a given energy threshold (≤10 kcal/mol (i), ≤5 kcal/mol (ii)) via DFT relaxation invariably led to the identification of the most stable structures as determined from high-resolution infrared (IR) spectroscopy at low temperature. The sGADFT method therefore constitutes a highly efficient route for the screening of realistic low-lying peptide structures in the gas phase as needed for instance for the interpretation and assignment of experimental IR spectra.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

A rotational study of the AlaAla dipeptide

Herein, we present the first rotational study of the AlaAla dipeptide, brought into the gas phase by laser ablation. Two different structures have been unveiled in the isolated environment of a supersonic expansion by Fourier transform microwave spectroscopy. These structures have been identified through their rotational and 14N quadrupole coupling constants. The flexibility of the -NH2 and -COOH ends allows the formation of strong intramolecular interactions giving rise to five- and seven-membered ring configurations.

Isolated neutral peptides

This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.

Combined IR/NIR and density functional theory calculations analysis of the solvent effects on frequencies and intensities of the fundamental and overtones of the C ═ O stretching vibrations of acetone and 2-hexanone

Vibrational overtone studies primarily focus on X-H stretching overtone transitions, where X is an atom like C, O, N, or S. In contrast, the studies on the C ═ O stretching overtones are very scattered. To advance the research in this field, we measured the fundamental, first, and second overtones of the C ═ O stretching vibration of acetone and 2-hexanone in n-hexane, CCl4, and CHCl3, as well as in the vapor phase using FT-IR/FT-NIR spectroscopy. Density functional theory (DFT) calculations have also been performed to help the assignment of the C ═ O stretching bands and to guide interpretation of the experimental results. It was found that the wavenumbers, absorption intensities, and oscillator strengths of the C ═ O stretching bands show marked solvent dependence. In the fundamental and the first overtone regions, the intensities of the C ═ O stretching vibration were found to be pronouncedly more intense than those of the C-H stretching vibration. In the second overtone region, the intensities of the C-H stretching vibration are comparable to those of the C ═ O stretching vibration. The theoretical and observed decrease in integrated intensity upon going from the fundamental to the first overtone of the C ═ O stretching vibration is around 50, which is significantly larger than those of the O-H, C-H, and S-H stretching vibration. Both the calculated and experimental results suggest that excessive weakness in the C ═ O stretching overtone was shown to be a result of both a low anharmonicity and a substantial reduction in the oscillator strength. These results provide new insight into our understanding of the C ═ O stretching vibration.

Mass-selected IR-VUV (118 nm) spectroscopic studies of radicals, aliphatic molecules, and their clusters

Mass-selected IR plus UV/VUV spectroscopy and mass spectrometry have been coupled into a powerful technique to investigate chemical, physical, structural, and electronic properties of radicals, molecules, and clusters. Advantages of the use of vacuum ultraviolet (VUV) radiation to create ions for mass spectrometry are its application to nearly all compounds with ionization potentials below the energy of a single VUV photon, its circumventing the requirement of UV chromophore group, its inability to ionize background gases, and its greatly reduced fragmenting capabilities. In this review, mass-selected IR plus VUV (118 nm) spectroscopy is introduced first in a general manner. Selected application examples of this spectroscopy are presented, which include the detections and structural analysis of radicals, molecules, and molecular clusters in a supersonic jet.

Vibrational spectroscopy and conformational structure of protonated polyalanine peptides isolated in the gas phase

The conformational structures of protonated polyalanine peptides, Ala(n)H(+), have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala(3)H(+), adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala(7)H(+), adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.

Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures

Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA, and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices, and turns, which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides.

Conformational preferences of an amyloidogenic peptide: IR spectroscopy of Ac-VQIVYK-NHMe

The (306)VQIVYK(311) sequence in the tau peptide is essential for the formation of intracellular amyloid fibrils related to Alzheimer's disease, where it forms interdigitating cross-beta-structures. The inherent conformational preferences of the capped hexapeptide Ac-VQIVYK-NHMe were characterized in the gas phase. IR/UV double-resonance spectroscopy of the peptide isolated in a cold molecular beam was used to probe the conformation of the neutral peptide. The influence of protonation at the lysine side chain was investigated at 298 K by characterizing the protonated peptide ion, Ac-VQIVYK(H(+))-NHMe, with IRMPD spectroscopy in the fingerprint and amide I/II band region in an FTICR mass spectrometer. The conformations for both neutral and protonated peptides were predicted by an extensive conformational search procedure followed by cluster analysis and then DFT calculations. Comparison of the experimental and computed IR spectra, with consideration of the relative energies, was used to assign the dominant conformations observed. The neutral peptide adopts a beta-hairpin-like conformation with two loosely extended peptide chains, demonstrating the preference of the sequence for extended beta-strand-like structures. In the protonated peptide, the lysine NH3(+) disrupts this extended conformation by binding to the backbone and induces a transition to a random-coil-like structure.

Imino Tautomers of Gas-Phase Guanine from Mid-Infrared Laser Spectroscopy

We reinvestigated the assignment of the three major guanine conformers detected via resonance enhanced two-photon ionization (R2PI) in supersonic expansions and present IR/UV double resonance spectra in the spectral region between 1500 and 1800 cm(-1). Comparison with B3LYP/TZVPP and RI-MP2/cc-pVQZ calculations shows that both conformers B and C are 7H-keto tautomers with an imine group in the 2-position. They differ only in the local conformation of the imine group but are otherwise identical. Conformer A is an amino-enol form with the OH group in the trans position.

Double-hybrid density functionals with long-range dispersion corrections: higher accuracy and extended applicability

The objective of this work is the further systematic improvement of the accuracy of Double-Hybrid Density Functionals (DHDF) that add non-local electron correlation effects to a standard hybrid functional by second-order perturbation theory (S. Grimme, J. Chem. Phys., 2006, 124, 034108). The only known shortcoming of these generally highly accurate functionals is an underestimation of the long-range dispersion (van der Waals) interactions. To correct this deficiency, we add a previously developed empirical dispersion term (DFT-D) to the energy expression but leave the electronic part of the functional untouched. Results are presented for the S22 set of non-covalent interaction energies, the G3/99 set of heat of formations and conformational energies of a phenylalanyl-glycyl-glycine peptide model. We furthermore propose seven hydrocarbon reactions with strong intramolecular dispersion contributions as a benchmark set for newly developed density functionals. In general, the proposed composite approach is for many chemically relevant properties of similar quality as high-level coupled-cluster treatments. A significant increase of the accuracy for non-covalent interactions is obtained and the corrected B2PLYP DHDF provides one of the lowest ever obtained Mean Absolute Deviations (MAD) for the S22 set (0.2-0.3 kcal mol(-1)). Unprecedented high accuracy is also obtained for the relative energies of peptide conformations that turn out to be very difficult. The significant improvements found for the G3/99 set (reduction of the MAD from 2.4 to 1.7 kcal mol(-1)) underline the importance of intramolecular dispersion effects in large molecules. In all tested cases the results from the standard B3LYP approach are also significantly improved, and we recommend the general use of dispersion corrections in DFT treatments.