Vibrational Signatures of Conformer-Specific Intramolecular Interactions in Protonated Tryptophan

IR and UV Spectroscopy of Gas-Phase Monohydrated Protonated Guanine

We use UV and infrared photodissociation spectroscopy to study monohydrated protonated guanine in a dual cryogenic ion trap spectrometer. The monohydrated complexes are formed through helium-mediated collisions between bare electrosprayed protonated guanine and low-pressure water vapor in a clustering trap maintained at 180 K, before being transferred to a quadrupole ion trap at 10 K. The spectrum of the monohydrated complex exhibits sharp vibronic transitions at the band origin and becomes broader and higher in intensity further in blue, which is very similar to protonated guanine but with a notable blue shift of ∼1850 cm-1 (∼0.23 eV). The UV hole-burning experiments showed that the vibronic bands recorded in the region of the band origin belong to a single conformer under our experimental conditions. The IR photodissociation spectrum in the 3000-3600 cm-1 range, with the aid of theoretical calculations (SCS-CC2/aug-cc-pVDZ), allowed us to assign the structure to the lowest energy N7-O conformer.

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

Micro Solvation Effect of Methanol on Excited-State Dynamics of Protonated Tryptophan and Dopamine

The electronic and vibrational cryogenic ion spectroscopy of protonated tryptophan (TrpH+) and dopamine (DAH+) complexed with methanol has been recorded. These two biological chromophores exhibit ultrafast photochemistry due to excited-state proton transfer (ESPT). We have established the relationship between the structure of the complexes and their photodynamics and compared them with recent results obtained in hydrated complexes. For TrpH+, there is no substantial change between methanol and water complexes; ESPT is hindered by a single solvent molecule. In the DAH+(MeOH)1 complex, the most stable conformer adopts a structure that prevents the direct interaction of the ammonium group of the side chain with the catechol ring, thus blocking the ESPT reaction. Such a ring structure is indeed a very minor populated conformer in the single-hydrated complex. The change in conformal stability between water and methanol clusters is due to a weak CH-π attractive interaction of the methyl group of methanol with the catechol.

Conformer-selective Photodynamics of TrpH+ -H2 O

The photodynamics of protonated tryptophan and its mono hydrated complex TrpH⁺ -H₂ O has been revisited. A combination of steady-state IR and UV cryogenic ion spectroscopies with picosecond pump-probe photodissociation experiments sheds new lights on the deactivation processes of TrpH⁺ and conformer-selected TrpH⁺ -H₂ O complex, supported by quantum chemistry calculations at the DFT and coupled-cluster levels for the ground and excited states, respectively. TrpH⁺ excited at the band origin exhibits a transient of less than 100 ps, assigned to the lifetime of the excited state proton transfer (ESPT) structure. The two experimentally observed conformers of TrpH⁺ -H₂ O have been assigned. A striking result arises from the conformer-selective photodynamics of TrpH⁺ -H₂ O, in which a single water molecule inserted in between the ammonium and the indole ring hinders the barrierless ESPT reaction responsible for the ultra-fast deactivation process observed in the other conformer and in bare TrpH⁺ .

Experimental techniques and terminology in gas-phase ion spectroscopy

This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas-phase action ion spectroscopy can make a large impact.

Cryogenic IR and UV spectroscopy of isomer-selected cytosine radical cation

The UV photodissociation of cryogenic-cooled isomer-selected cytosine–silver complex leads to the production of cytosine radical cation without isomerization.

Development of a photoinduced fragmentation ion trap for infrared multiple photon dissociation spectroscopy

RATIONALE

Methods for isomer discrimination by mass spectroscopy are of increasing interest. Here we describe the development of a three-dimensional ion trap for infrared multiple photon dissociation (IRMPD) spectroscopy that enables the acquisition of the infrared spectrum of selected ions in the gas phase. This system is suitable for the study of a myriad of chemical systems, including isomer mixtures.

METHODS

A modified three-dimensional ion trap was coupled to a CO₂ laser and an optical parametric oscillator/optical parametric amplifier (OPO/OPA) system operating in the range 2300 to 4000 cm^-1 . Density functional theory vibrational frequency calculations were carried out to support spectral assignments.

RESULTS

Detailed descriptions of the interface between the laser and the mass spectrometer, the hardware to control the laser systems, the automated system for IRMPD spectrum acquisition and data management are presented. The optimization of the crystal position of the OPO/OPA system to maximize the spectroscopic response under low-power laser radiation is also discussed.

CONCLUSIONS

OPO/OPA and CO₂ laser-assisted dissociation of gas-phase ions was successfully achieved. The system was validated by acquiring the IRMPD spectra of model species and comparing with literature data. Two isomeric alkaloids of high economic importance were characterized to demonstrate the potential of this technique, which is now available as an open IRMPD spectroscopy facility in Brazil.

Time-Dependent Perspective for the Intramolecular Couplings of the N–H Stretches of Protonated Tryptophan

Quasi-classical direct dynamics simulations, performed with the B3LYP-D3/cc-pVDZ electronic structure theory, are reported for vibrational relaxation of the three NH stretches of the −NH₃⁺ group of protonated tryptophan (TrpH⁺), excited to the n = 1 local mode states. The intramolecular vibrational energy relaxation (IVR) rates determined for these states, from the simulations, are in good agreement with the experiment. In accordance with the experiment, IVR for the free NH stretch is slowest, with faster IVR for the remaining two NH stretches which have intermolecular couplings with an O atom and a benzenoid ring. For the free NH and the NH coupled to the benzenoid ring, there are beats (i.e., recurrences) in their relaxations versus time. For the free NH stretch, 50% of the population remained in n = 1 when the trajectories were terminated at 0.4 ps. IVR for the free NH stretch is substantially slower than for the CH stretch in benzene. The agreement found in this study between quasi-classical direct dynamics simulations and experiments indicates the possible applicability of this simulation method to larger biological molecules. Because IVR can drive or inhibit reactions, calculations of IVR time scales are of interest, for example, in unimolecular reactions, mode-specific chemistry, and many photochemical processes.

Revealing Single-Bond Anomeric Selectivity in Carbohydrate-Protein Interactions

The noncovalent binding of proteins to glycans is amazingly selective to the isoforms of carbohydrates, including α/β anomers that coexist in solution. We isolate in the gas phase and study at the atomic level the simplest model system: noncovalent complexes of monosaccharide α/β-GalNAc and protonated aromatic molecule tyramine. IR/UV cold ion spectroscopy and quantum chemistry calculations jointly solve the structures of the two complexes. Although the onsets of the measured UV absorptions of the complexes differ significantly, the networks of H bonds in both complexes appear identical and do not include the anomeric hydroxyl. The detailed analysis reveals that, through inductive polarization, the α- to β-reorientation of this group nevertheless reduces the length of one remote short intermolecular H-bond by 0.03 Å. Although small, this change substantially strengthens the bond, thus contributing to the anomeric selectivity of the binding.

Gas-phase structures reflect the pain-relief potency of enkephalin peptides

We use cold ion spectroscopy and quantum-chemical computations to solve the structures of opioid peptides enkephalins in the gas phase. The derived structural parameters clearly correlate with the known pharmacological efficiency of the studied drugs, suggesting that gas-phase methods, perhaps, can be used for predicting the relative potency of ligand drugs that target the hydrophobic pockets of receptors.

Cryogenic Ion Spectroscopy for Identification of Monosaccharide Anomers

We combine conformer-selective, cryogenic infrared spectroscopy, quantum mechanical computations, and ¹⁸O substitution at the reducing end to determine the structural preferences of protonated glucosamine in the gas phase. Cryogenic infrared-infrared (IR-IR) double resonance spectroscopy of helium-tagged, protonated glucosamine provides vibrational fingerprints of individual conformers, and ¹⁸O isotopic labeling facilitates the match with computed structures and provides a selective probe of the anomeric hydroxyl. This is key for using vibrational spectroscopy for glycan analysis and determining the generality of anomeric memory during glycosidic bond cleavage.

On the choice of coordinates in anharmonic theoretical vibrational spectroscopy: Harmonic vs. anharmonic coupling in vibrational configuration interaction

By a suitable choice of coordinates, the computational effort required for calculations of anharmonic vibrational spectra can be reduced significantly. By using suitable localized-mode coordinates obtained from an orthogonal transformation of the conventionally used normal-mode coordinates, anharmonic couplings between modes can be significantly reduced. However, such a transformation introduces harmonic couplings between the localized modes. To elucidate the role of these harmonic couplings, we consider the vibrational self-consistent field (VSCF)/vibrational configuration interaction (VCI) calculations for both few-mode model systems and for ethene as a molecular test case. We show that large harmonic couplings can result in significant errors in localized-mode L-VSCF/L-VCI calculations and study the convergence with respect to the size of the VCI excitation space. To further elucidate the errors introduced by harmonic couplings, we discuss the connection between L-VSCF/L-VCI and vibrational exciton models. With the help of our results, we propose an algorithm for the localization of normal modes in suitable subsets that are chosen to strictly limit the errors introduced by the harmonic couplings while still leading to maximally localized modes.

Vibrational Predissociation Spectroscopy of Cold Protonated Tryptophan with Different Messenger Tags

Vibrational spectra of protonated tryptophan were recorded by predissociation of H₂ messenger tags using cryogenic ion traps. We explore the issue of messenger induced spectral changes by solvating TrpH⁺(H₂) _n with n = 1-5 to obtain single photon vibrational spectra of TrpH⁺ and of its partly deuterated isotopomer in the spectral region of 800-4400 cm^-1. Depending on the number of messenger molecules, the spectra of several conformational isomers associated with multiple H₂ binding locations along with two natural conformations of TrpH⁺ were found using the two photon MS³IR² conformational hole burning method. Most probable messenger positions were established by comparison with predictions from DFT calculations on various candidate structures. Mechanical anharmonicity effects associated with the charged amino group were modeled by Born-Oppenheimer ab initio molecular dynamics. The spectra of TrpH⁺(H₂O) _m=1,2, recorded by infrared multiphoton dissociation (IRMPD), reveal broad features in the NH stretching region of the NH₃⁺ group, indicating strong hydrogen bonding in acceptor-donor configuration with the benzene ring for the first water molecule, while the second water appears to attach to a less strongly perturbing site, yielding unique transitions associated with the free OH stretching fundamentals. We discuss the structural deformations induced by the water molecules and compare our results to recent experiments on similar hydrated cationic systems.

Peptide Bond Ultraviolet Absorption Enables Vibrational Cold-Ion Spectroscopy of Nonaromatic Peptides

Peptide-bond VUV absorption is inherent to all proteins and peptides. Although widely exploited in top-down proteomics for photodissociation, this absorption has never been spectroscopically characterized in the gas phase. We have measured VUV/UV photofragmentation spectrum of a single peptide bond in a cryogenically cold protonated dipeptide. Although the spectrum appears to be very broadband and structureless, vibrational pre-excitation of this and even larger cold peptides significantly increases the UV dissociation yield for some of their photofragments. We use this effect to extend the technique of IR-UV photofragmentation vibrational spectroscopy, developed for aromatic peptides, to nonaromatic ones and demonstrate measurements of conformation-specific and nonspecific IR spectra for di- to hexa-peptides.

Ribeiro FW, Cervi G, C. Correra T. Evaluation of Common Theoretical Methods for Predicting Infrared Multiphotonic Dissociation Vibrational Spectra of Intramolecular Hydrogen-Bonded Ions

Infrared photodissociation analyses are supported by theoretical calculations that allow a trustworthy interpretation of experimental spectra of gaseous ions. B3LYP calculations are the most prominent method used to model IR spectra, as detailed in our bibliographic survey. However, this and other commonly used methods are known to provide inaccurate energy values and geometries, especially when it comes to long-range interactions, such as intramolecular H-bonds, which show increased anharmonicity. Therefore, we evaluated some of the most commonly used density functional theory methods (B3LYP, CAM-B3LYP, and M06-2X) and basis sets (6-31+G(d,p), 6-311++G(d,p), 6-311++G(3df,2pd), aug-cc-pVDZ, and aug-cc-pVTZ), including anharmonicity and dispersion corrections. The results were compared to MP2 calculations and to experimental high-frequency (2000-4000 cm-1) IR multiphotonic dissociation (IRMPD) spectra of two protonated model molecules containing intramolecular hydrogen bonds: biotin and tryptophan. M06-2X/6-31+G(d,p) was shown to be the most cost-effective level of theory, whereas CAM-B3LYP was the most efficient method to describe the van der Waals interactions. The use of the dispersion correction D3, proposed by Grimme, improved the description of O-H vibrations involved in H-bonding but worsened the description of N-H stretches. Anharmonic calculations were shown to be extremely expensive when compared to other approaches. The efficiencies of well-established scaling factors (SFs) in opposition to sample-dependent SFs were also discussed and the use of fitted SFs were shown to be the most cost-effective approach to predict IRMPD spectra. M06-2X/6-31+G(d,p) and CAM-B3LYP/aug-cc-pVDZ were also tested against the fingerprint region. Our results suggest that these methods can also be used for analysis in this lower frequency range and should be regarded as the methods of choice for cost-effective IRMPD simulations rather than the ubiquitous B3LYP method, especially when further molecular properties are needed.

Structural Rearrangement by Isomer-Specific Infrared Excitation in the Neutral Isolated Dihydrated Cluster of 3-Hydroxyflavone

Isomer-specific, IR-induced reactions in the electronic ground state (S₀) can be of great interest to control reaction pathways. Here we show a first example of these reactions with isomer-specific excitation and formation of a new isomer under isolated conditions in a molecular beam experiment. The investigated dihydrated cluster of 3-hydroxyflavone forms two isomers, I and D, in the S₀ state. We show that only a mode-specific excitation of isomer I leads to a structural rearrangement yielding an isomer that has not been identified so far. This isomer is assigned in comparison to quantum chemical calculations. The experiments are performed by applying an IR/IR method in combination with a mass-selective resonant two-photon ionization (R2PI) process. Usually these kinds of IR/IR/R2PI methods are chosen to discriminate isomers; here it is demonstrated that this powerful method can also be applied for analysis of IR-induced reactions probed by an IR/R2PI process.

Infrared ion spectroscopy: an analytical tool for the study of metabolites

Vibrational ion spectroscopy techniques coupled with mass spectrometry are applied to standard metabolites as a proof-of-principle demonstration for the structural identification of unknown metabolites. The traditional room temperature infrared multiple photon dissociation (IRMPD) spectroscopy technique is shown to differentiate chemical moieties in isobaric and isomeric variants. These results are compared to infrared spectra of cryogenically cooled analyte ions, showing enhanced spectral resolution, and thus also improved differentiation between closely related molecules, such as isomers. The cryogenic spectroscopy is effected in a recently developed mass-selective cryogenic linear ion trap, which is capable of high sensitivity and the ability to measure the IR spectra of multiple analytes simultaneously.

Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A

Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.

Identification of isoforms of aspartic acid residues in peptides by 2D UV-MS fingerprinting of cold ions

We use 2D UV-MS cold-ion spectroscopy for the identification of l-Asp, d-Asp, l-isoAsp and d-isoAsp residues in a fragment peptide derived from the hormone protein amylin.