Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics.

A technique capable of label-free detection, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of native biomolecules in intact specimens. However, MSI has often been precluded from single-cell applications due to the spatial resolution limit set forth by the physical and instrumental constraints of the method. By taking advantage of the reversible interaction between the analytes and a superabsorbent hydrogel, we have developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome the spatial resolution limits of modern mass spectrometers. With GAMSI, we show that the spatial resolution of MALDI-MSI can be enhanced ~3-6-fold to the sub-micrometer level without changing the existing mass spectrometry hardware or analysis pipeline. This approach will vastly enhance the accessibility of MSI-based spatial analysis at the cellular scale.

Untargeted Pixel-by-Pixel Imaging of Metabolite Ratio Pairs as a Novel Tool for Biomedical Discovery in Mass Spectrometry Imaging.

Mass spectrometry imaging (MSI) is a powerful technology used to define the spatial distribution and relative abundance of structurally identified and yet-undefined metabolites across tissue cryosections. While numerous software packages enable pixel-by-pixel imaging of individual metabolites, the research community lacks a discovery tool that images all metabolite abundance ratio pairs. Importantly, recognition of correlated metabolite pairs informs discovery of unanticipated molecules contributing to shared metabolic pathways, uncovers hidden metabolic heterogeneity across cells and tissue subregions, and indicates single-timepoint flux through pathways of interest. Here, we describe the development and implementation of an untargeted R package workflow for pixel-by-pixel ratio imaging of all metabolites detected in an MSI experiment. Considering untargeted MSI studies of murine brain and embryogenesis, we demonstrate that ratio imaging minimizes systematic data variation introduced by sample handling and instrument drift, markedly enhances spatial image resolution, and reveals previously unrecognized metabotype-distinct tissue regions. Furthermore, ratio imaging facilitates identification of novel regional biomarkers and provides anatomical information regarding spatial distribution of metabolite-linked biochemical pathways. The algorithm described herein is applicable to any MSI dataset containing spatial information for metabolites, peptides or proteins, offering a potent tool to enhance knowledge obtained from current spatial metabolite profiling technologies.

The influence of eye model parameter variations on simulated eye-tracking outcomes.

The simulated data used in eye-tracking-related research has been largely generated using normative eye models with little consideration of how the variations in eye biometry found in the population may influence eye-tracking outcomes. This study investigated the influence that variations in eye model parameters have on the ability of simulated data to predict real-world eye-tracking outcomes. The real-world experiments performed by two pertinent comparative studies were replicated in a simulated environment using a highcomplexity stochastic eye model that includes anatomically accurate distributions of eye biometry parameters. The outcomes showed that variations in anterior corneal asphericity significantly influence simulated eye-tracking outcomes of both interpolation and model-based gaze estimation algorithms. Other, more commonly varied parameters such as the corneal radius of curvature and foveal offset angle had little influence on simulated outcomes.

Rewiring of cortical glucose metabolism fuels human brain cancer growth.

The brain avidly consumes glucose to fuel neurophysiology. Cancers of the brain, such as glioblastoma (GBM), lose aspects of normal biology and gain the ability to proliferate and invade healthy tissue. How brain cancers rewire glucose utilization to fuel these processes is poorly understood. Here we perform infusions of 13 C-labeled glucose into patients and mice with brain cancer to define the metabolic fates of glucose-derived carbon in tumor and cortex. By combining these measurements with quantitative metabolic flux analysis, we find that human cortex funnels glucose-derived carbons towards physiologic processes including TCA cycle oxidation and neurotransmitter synthesis. In contrast, brain cancers downregulate these physiologic processes, scavenge alternative carbon sources from the environment, and instead use glucose-derived carbons to produce molecules needed for proliferation and invasion. Targeting this metabolic rewiring in mice through dietary modulation selectively alters GBM metabolism and slows tumor growth. Significance: This study is the first to directly measure biosynthetic flux in both glioma and cortical tissue in human brain cancer patients. Brain tumors rewire glucose carbon utilization away from oxidation and neurotransmitter production towards biosynthesis to fuel growth. Blocking these metabolic adaptations with dietary interventions slows brain cancer growth with minimal effects on cortical metabolism.

Dissociation Kinetics in Quadrupole Ion Traps: Effective Temperatures under Dipolar DC Collisional Activation Conditions.

Ions stored in an electrodynamic ion trap can be forced from the center of the ion trap to regions of higher radio frequency (RF) electric fields by exposing them to a dipolar DC (DDC) potential applied across opposing electrodes. Such ions absorb power from the trapping RF field, resulting in increased ripple motion at the frequency of the trapping RF. When a bath gas is present, ions undergo energetic collisions that result in "RF-heating" sufficient to induce fragmentation. DDC is therefore a broad-band (i.e., mass-to-charge-independent) means for collisional activation in ion traps with added bath gas. Under appropriate conditions, the internal energy distribution of an ion population undergoing dissociation can be approximated with an effective temperature, Teff. In such cases, it is possible to determine thermal activation parameters, such as Arrhenius activation energies and A-factors, by measuring dissociation kinetics. In this work, the well-studied thermometer ion, protonated leucine enkephalin, was subjected to DDC activation under rapid energy exchange conditions and in two separate bath gases, N2 and Ar, to measure Teff as a function of the ratio of DDC and RF voltages. As a result, an empirically derived calibration was generated to link experimental conditions to Teff. It was also possible to quantitatively evaluate a model described by Tolmachev et al. that can be used to predict Teff. It was found that the model, which was derived under the assumption of an atomic bath gas, accurately predicts Teff when Ar was used as the bath gas but overestimates Teff when N2 was the bath gas. Adjustment of the Tolmachev et al. model for a diatomic gas resulted in an underestimate of Teff. Thus, use of an atomic gas can provide accurate activation parameters, while an empirical correction factor should be used to generate activation parameters using N2.

Structural elucidation and isomeric differentiation/quantitation of monophosphorylated phosphoinositides using gas-phase ion/ion reactions and dissociation kinetics.

Phosphoinositides, phosphorylated derivatives of phosphatidylinositols, are essential signaling phospholipids in all mammalian cellular membranes. With three known phosphorylated derivatives of phosphatidylinositols at the 3-, 4-, and 5-positions along the myo-inositol ring, various fatty acyl chain lengths, and varying degrees of unsaturation, numerous isomers can be present. It is challenging for shotgun-MS to accurately identify and characterize phosphoinositides and their isomers using the most readily available precursor ion types. To overcome this challenge, novel gas-phase ion/ion chemistry was used to expand the range of precursor ion-types for subsequent structural characterization of phosphoinositides using shot-gun tandem mass spectrometry. The degree of phosphorylation and fatty acyl sum composition are readily obtained by ion-trap CID of deprotonated phosphoinositides. Carbon-carbon double bond position of the fatty acyl chains can be localized via a charge inversion ion/ion reaction. Utilizing sequential ion/ion reactions and subsequent activation yields product ion information that is of limited utility for phosphorylation site localization. However, the kinetics of dissociation allowed for isomeric differentiation of the position of the phosphate group. Furthermore, employing the same kinetics method, relative quantitative information was gained for the isomeric species.

Conformer-Specific Spectroscopy and IR-Induced Isomerization of a Model γ-Peptide: Ac-γ4-Phe-NHMe.

Single-conformation IR and UV spectroscopy of the prototypical capped γ-peptide Ac-γ4-Phe-NHMe (γ4F) was carried out under jet-cooled conditions in the gas phase in order to understand its innate conformational preferences in the absence of a solvent. We obtained conformer-specific IR and UV spectra and compared the results with calculations to make assignments and explore the differences between the γ2- and γ4-substituted molecules. We found four conformers of γ4F in our experiment. Three conformers form nine-membered hydrogen-bonded rings (C9) enclosed by an NH···O═C H-bond but differing in their phenyl ring positions (a, g+, and g-). The fourth conformer forms a strained seven-membered hydrogen-bonded ring in which the amide groups lie in a nominally anti-parallel arrangement stacked on top of one another (labeled S7). This conformer is a close analogue of the amide-stacked conformer (S) found previously in γ2F, in which the Phe side chain is substituted at the γ2 position, Ac-γ2-Phe-NHMe (J. Am. Chem. Soc. 2009, 131, 14243-14245). IR population transfer spectroscopy was used to determine the fractional abundances of the γ4F conformers in the expansion. A combination of force field and density functional theory calculations is used to map out the conformational potential energy surfaces for γ4F and compare it with its γ2F counterpart. Based on this analysis, the phenyl ring prefers to take up structures that facilitate NH···π interactions in γ4F or avoid phenyl interactions with the C═O group in γ2F. The disconnectivity graph for γ4F reveals separate basins associated with the C9 and amide-stacked conformational families, which are separated by a barrier of about 42 kJ/mol. The overall shape of the potential energy surface bears a resemblance to peptides and proteins that have a misfolding pathway that competes with the formation of the native structure.

Gas-Phase Covalent Bond Formation via Nucleophilic Substitution: A Dissociation Kinetics Study of Leaving Groups, Isomeric R Groups, and Nucleophilic Sites.

Nucleophilic substitution covalent modification ion/ion reactions were carried out in a linear quadrupole ion trap between the doubly protonated peptides KGAILKGAILR, RARARAA, and RKRARAA and isomers of either singly deprotonated 3- or 4-sulfobenzoic acid (n-SBA) esterified with either N-hydroxysuccinimide (NHS) or 1-hydroxy-7-aza-benzotriazole (HOBt). The cation/anion attachment product, through which the covalent reaction occurs, was isolated and subjected to dipolar DC (DDC) activation to generate covalently modified product over the ranges of DDC activation energies and times. The resulting survival yields were used to determine reaction rates, and Tolmachev's effective ion temperature was used to extract Arrhenius and Eyring activation parameters. It was found that the kinetics determined under these conditions are highly sensitive to the identities and locations of the nucleophilic sites on the peptides, the leaving groups on the reagent, and the location of the attachment sites on the reagent and analyte. Depending upon the identity of the analyte/reagent combination, significant variations in activation energy or entropy (or both) were both found to underlie the measured rate differences. The determination of dissociation kinetics under DDC conditions and application of Tolmachev's effective ion temperature treatment enables unique insights into the dynamics of gas-phase covalent bond formation via ion/ion reactions.

RNAi for Western Corn Rootworm Management: Lessons Learned, Challenges, and Future Directions.

The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is considered one of the most economically important pests of maize (Zea mays L.) in the United States (U.S.) Corn Belt with costs of management and yield losses exceeding USD ~1-2 billion annually. WCR management has proven challenging given the ability of this insect to evolve resistance to multiple management strategies including synthetic insecticides, cultural practices, and plant-incorporated protectants, generating a constant need to develop new management tools. One of the most recent developments is maize expressing double-stranded hairpin RNA structures targeting housekeeping genes, which triggers an RNA interference (RNAi) response and eventually leads to insect death. Following the first description of in planta RNAi in 2007, traits targeting multiple genes have been explored. In June 2017, the U.S. Environmental Protection Agency approved the first in planta RNAi product against insects for commercial use. This product expresses a dsRNA targeting the WCR snf7 gene in combination with Bt proteins (Cry3Bb1 and Cry34Ab1/Cry35Ab1) to improve trait durability and will be introduced for commercial use in 2022.

An overview of biological applications and fundamentals of new inlet and vacuum ionization technologies.

RATIONALE: The developments of new ionization technologies based on processes previously unknown to mass spectrometry (MS) have gained significant momentum. Herein we address the importance of understanding these unique ionization processes, demonstrate the new capabilities currently unmet by other methods, and outline their considerable analytical potential. METHODS: The inlet and vacuum ionization methods of solvent-assisted ionization (SAI), matrix-assisted ionization (MAI), and laserspray ionization can be used with commercial and dedicated ion sources producing ions from atmospheric or vacuum conditions for analyses of a variety of materials including drugs, lipids, and proteins introduced from well plates, pipet tips and plate surfaces with and without a laser using solid or solvent matrices. Mass spectrometers from various vendors are employed. RESULTS: Results are presented highlighting strengths relative to ionization methods of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization. We demonstrate the utility of multi-ionization platforms encompassing MAI, SAI, and ESI and enabling detection of what otherwise is missed, especially when directly analyzing mixtures. Unmatched robustness is achieved with dedicated vacuum MAI sources with mechanical introduction of the sample to the sub-atmospheric pressure (vacuum MAI). Simplicity and use of a wide array of matrices are attained using a conduit (inlet ionization), preferably heated, with sample introduction from atmospheric pressure. Tissue, whole blood, urine (including mouse, chicken, and human origin), bacteria strains and chemical on-probe reactions are analyzed directly and, especially in the case of vacuum ionization, without concern of carryover or instrument contamination. CONCLUSIONS: Examples are provided highlighting the exceptional analytical capabilities associated with the novel ionization processes in MS that reduce operational complexity while increasing speed and robustness, achieving mass spectra with low background for improved sensitivity, suggesting the potential of this simple ionization technology to drive MS into areas currently underserved, such as clinical and medical applications.

Resolving Isomers of Star-Branched Poly(Ethylene Glycols) by IMS-MS Using Multiply Charged Ions.

Ion mobility spectrometry (IMS) mass spectrometry (MS) centers on the ability to separate gaseous structures by size, charge, shape, and followed by mass-to-charge (m/z). For oligomeric structures, improved separation is hypothesized to be related to the ability to extend structures through repulsive forces between cations electrostatically bonded to the oligomers. Here we show the ability to separate differently branched multiply charged ions of star-branched poly(ethylene glycol) oligomers (up to 2000 Da) regardless of whether formed by electrospray ionization (ESI) charged solution droplets or from charged solid particles produced directly from a surface by matrix-assisted ionization. Detailed structural characterization of isomers of the star-branched compositions was first established using a home-built high-resolution ESI IMS-MS instrument. The doubly charged ions have well-resolved drift times, achieving separation of isomers and also allowing differentiation of star-branched versus linear oligomers. An IMS-MS "snapshot" approach allows visualization of architectural dispersity and (im)purity of samples in a straightforward manner. Analyses capabilities are shown for different cations and ionization methods using commercially available traveling wave IMS-MS instruments. Analyses directly from surfaces using the new ionization processes are, because of the multiply charging, not only associated with the benefits of improved gas-phase separations, relative to that of ions produced by matrix-assisted laser desorption/ionization, but also provide the potential for spatially resolved measurements relative to ESI and other ionization methods.

The missing NH stretch fundamental in S1 methyl anthranilate: IR-UV double resonance experiments and local mode theory.

The infrared spectra of jet-cooled methyl anthranilate (MA) and the MA-H2O complex are reported in both S0 and S1 states, recorded using fluorescence-dip infrared (FDIR) spectroscopy under jet-cooled conditions. Using a combination of local mode CH stretch modeling and scaled harmonic vibrational character, a near-complete assignment of the infrared spectra is possible over the 1400-3700 cm-1 region. While the NH stretch fundamentals are easily observed in the S0 spectrum, in the S1 state, the hydrogen bonded NH stretch shift is not readily apparent. Scaled harmonic calculations predict this fundamental at just below 2900 cm-1 with an intensity around 400 km mol-1. However, the experimental spectrum shows no evidence of this transition. A local mode theory is developed in which the NH stretch vibration is treated adiabatically. Minimizing the energy of the corresponding stretch state with one quantum of excitation leads to a dislocation of the H atom where there is equal sharing between N and O atoms. The sharing occurs as a result of significant molecular arrangement due to strong coupling of this NH stretch to other internal degrees of freedom and in particular to the contiguous HNC bend. A two-dimensional model of the coupling between the NH stretch and this bend highlights important nonlinear effects that are not captured by low order vibrational perturbation theory. In particular, the model predicts a dramatic dilution of the NH stretch oscillator strength over many transitions spread over more than 1000 cm-1, making it difficult to observe experimentally.

Environmental Fate and Dissipation of Applied dsRNA in Soil, Aquatic Systems, and Plants.

Two primary use patterns exist for dsRNA-based products for crop protection: in planta produced dsRNA such as in a genetically engineered (GE) crop; and topically applied dsRNA such as a spray application. To enable effective environmental risk assessments for these products, dsRNA must be successfully measured in relevant environmental compartments (soil, sediment, surface water) to provide information on potential exposure. This perspective reviews results from numerous environmental fate and degradation studies with topically applied unformulated dsRNAs to demonstrate the high lability of these molecules and low potential for persistence in the environment. Additionally, we report on results of a pilot study of topically applied dsRNA on soybean plants demonstrating similar rapid degradation under field conditions. Microbial degradation of nucleic acids in environmental compartments has been shown to be a key driver for this lack of persistence. In fact, the instability of dsRNA in the environment has posed a challenge for the development of commercial topically-applied products. Formulations or other approaches that mitigate environmental degradation may lead to development of commercially successful products but may change the known degradation kinetics of dsRNAs. The formulation of these products and the resultant impacts on the stability of the dsRNA in environmental compartments will need to be addressed using problem formulation and product formulation testing may be required on a case by case basis to ensure an effective risk assessment.

New mass spectrometry concepts for characterization of synthetic polymers and additives.

RATIONALE: New ionization processes have been developed for biological mass spectrometry (MS) in which the matrix lifts the nonvolatile analyte into the gas phase as ions without any additional energy input. We rationalized that additional fundamental knowledge is needed to assess analytical utility for the field of synthetic polymers and additives. METHODS: Different mass spectrometers (Thermo Orbitrap (Q-)Exactive (Focus); Waters SYNAPT G2(S)) were employed. The formation of multiply charged polymer ions upon exposure of the matrix/analyte(/salt) sample to sub-atmospheric pressure directly from the solid state and surfaces facilitates the use of advanced mass spectrometers for detection of polymeric materials including consumer products (e.g., gum). RESULTS: Astonishingly, using nothing more than a small molecule matrix compound (e.g., 2-methyl-2-nitropropane-1,3-diol or 3-nitrobenzonitrile) and a salt (e.g., mono- or divalent cation(s)), such samples upon exposure to sub-atmospheric pressure transfer nonvolatile polymers and nonvolatile salts into the gas phase as multiply charged ions. These successes contradict the conventional understanding of ionization in MS, because can nonvolatile polymers be lifted in the gas phase as ions not only by as little as a volatile matrix but also by the salt required for ionizing the analyte through noncovalent metal cation adduction(s). Prototype vacuum matrix-assisted ionization (vMAI) and automated sources using a contactless approach are demonstrated for direct analyses of synthetic polymers and plasticizers, minimizing the risk of contamination using direct sample introduction into the mass spectrometer vacuum. CONCLUSIONS: Direct ionization methods from surfaces without the need of high voltage, a laser, or even applied heat are demonstrated for characterization of detailed materials using (ultra)high-resolution and accurate mass measurements enabled by the multiply charged ions extending the mass range of high-performance mass spectrometers and use of a split probe sample introduction device. Our vision is that, with further development of fundamentals and dedicated sources, both spatial- and temporal-resolution measurements are within reach if sensitivity is addressed for decreasing sample-size measurements.

Dissipation of DvSnf7 RNA from Late-Season Maize Tissue in Aquatic Microcosms.

The commercialization of RNA-based agricultural products requires robust ecological risk assessments. Ecological risk is operationally defined as a function of exposure and adverse effects. Information on the environmental fate of RNA-based plant-incorporated protectants is essential to define routes and duration of exposure to potentially sensitive nontarget organisms. Providing these details in problem formulation helps focus the ecological risk assessment on the relevant species of concern. Postharvest plant residue is often considered to be the most significant route of exposure for genetically modified crops to adjacent aquatic environments. Previous studies have shown that DvSnf7 RNA from SmartStax PRO maize dissipates rapidly in both terrestrial and aquatic environments. Although these studies suggest that direct exposure to DvSnf7 RNA is likely to be low, little is known regarding the fate of DvSnf7 RNA produced in plants after entering an aquatic environment. This exposure scenario is relevant to detritivorous aquatic invertebrates that process conditioned maize tissues that enter aquatic environments. To assess potential exposure to shredders, dissipation of DvSnf7 RNA expressed maize tissue was evaluated following immersion in microcosms containing sediment and water. Concentrations of DvSnf7 RNA in the tissue were measured over a duration of 21 d. The DvSnf7 RNA dissipated rapidly from immersed maize tissue and was undetectable in the tissues after 3 d. Concentrations of DvSnf7 RNA found in tissue as well as calculated water column concentrations were below levels known to elicit effects in a highly sensitive surrogate species, supporting the conclusion of minimal risk to aquatic nontarget organisms. Environ Toxicol Chem 2020;39:1032-1040. © 2020 SETAC.

Vibronic spectroscopy of methyl anthranilate and its water complex: hydrogen atom dislocation in the excited state.

Laser-induced fluorescence (LIF) excitation, dispersed fluorescence (DFL), UV-UV-hole burning, and UV-depletion spectra have been collected on methyl anthranilate (MA, methyl 2-aminobenzoate) and its water-containing complex (MA-H2O), under jet-cooled conditions in the gas phase. As a close structural analog of a sunscreen agent, MA has a strong absorption due to the S0-S1 transition that begins in the UV-A region, with the electronic origin at 28 852 cm-1 (346.6 nm). Unlike most sunscreens that have fast non-radiative pathways back to the ground state, MA fluoresces efficiently, with an excited state lifetime of 27 ns. Relative to methyl benzoate, inter-system crossing to the triplet manifold is shut off in MA by the strong intramolecular NHO[double bond, length as m-dash]C H-bond, which shifts the 3nπ* state well above the 1ππ* S1 state. Single vibronic level DFL spectra are used to obtain a near-complete assignment of the vibronic structure in the excited state. Much of the vibrational structure in the excitation spectrum is Franck-Condon activity due to three in-plane vibrations that modulate the distance between the NH2 and CO2Me groups, ν33 (421 cm-1), ν34 (366 cm-1), and ν36 (179 cm-1). Based on the close correspondence between experiment and theory at the TD-DFT B3LYP-D3BJ/def2TZVP level of theory, the major structural changes associated with electronic excitation are evaluated, leading to the conclusion that the major motion is a reorientation and constriction of the 6-membered H-bonded ring closed by the intramolecular NHO[double bond, length as m-dash]C H-bond. This leads to a shortening of the NHO[double bond, length as m-dash]C H-bond distance from 1.926 Å to 1.723 Å, equivalent to about a 25% reduction in the HO distance compared to full H-atom transfer. As a result, the excited state process near the S1 origin is a hydrogen atom dislocation that is brought about primarily by heavy atom motion, since the shortened H-bond distance results from extensive heavy-atom motion, with only a 0.03 Å increase in the NH bond length relative to its ground state value.

Single-Conformation Spectroscopy of Capped Aminoisobutyric Acid Dipeptides: The Effect of C-Terminal Cap Chromophores on Conformation.

Aminoisobutyric acid (Aib) oligomers are known to form racemic mixtures of enantiomeric left- and right-handed structures. The introduction of a chiral cap converts the enantiomeric structures into diastereomers that, in principle, afford spectroscopic differentiation. Here, we screen different C-terminal caps based on a model Aib dipeptide using double resonance laser spectroscopy in the gas phase to record IR and UV spectra of individual conformations present in the supersonic expansion: NH-benzyl (NHBn) as a reference structure because of its common use as a fluorophore in similar studies, NH- p-fluorobenzyl (NHBn-F), and α-methylbenzylamine (AMBA). For both the NHBn and NHBn-F caps, a single conformer is observed, with infrared spectra assignable to an enantiomeric pair of type II/II' ß-turns in these molecules lacking a chiral center. The higher oscillator strength of the NHBn-F cap enabled UV-UV hole burning, not readily accomplished with the NHBn cap. The AMBA-capped structure, with its chiral center, produced two unique conformers, one of which was a nearly identical left-handed type II ß-turn, while the minor conformer is assigned to a C7-C7 sequential double ring, which is an emergent form of a 27-ribbon. Although not observed, the type II' ß-turn diastereomer, with opposite handedness, is calculated to be 11 kJ/mol higher in energy, a surprisingly large difference. This destabilization is attributed primarily to steric interference between the C-terminal acyl oxygen of the peptide and the chirality-inducing methyl of the AMBA group. Last, computational evidence indicates that the use of an N-terminal aromatic cap hinders the formation of a 310-helix in Ac-Aib2 dipeptides.

Conformation-Specific Spectroscopy of Asparagine-Containing Peptides: Influence of Single and Adjacent Asn Residues on Inherent Conformational Preferences.

The infrared and ultraviolet spectra of a series of capped asparagine-containing peptides, Ac-Asn-NHBn, Ac-Ala-Asn-NHBn, and Ac-Asn-Asn-NHBn, have been recorded under jet-cooled conditions in the gas phase in order to probe the influence of the Asn residue, with its -CH2-C(═O)-NH2 side chain, on the local conformational preferences of a peptide backbone. The double-resonance methods of resonant ion-dip infrared (RIDIR) spectroscopy and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy were used to record single-conformation spectra in the infrared and ultraviolet, respectively, free from interference from other conformations present in the molecular beam. Ac-Asn-NHBn spreads its population over two conformations, both of which are stabilized by a pair of H-bonds that form a bridge between the Asn carboxamide group and the NH and C═O groups on the peptide backbone. In one the peptide backbone engages in a 7-membered H-bonded ring (labeled C7eq), thereby forming an inverse γ-turn, stabilized by a C6/C7 Asn bridge. In the other the Asn carboxamide group forms a C8/C7 H-bonded bridge with the carboxamide group facing in the opposite direction across an extended peptide backbone involving a C5 interaction. Both Ac-Ala-Asn-NHBn and Ac-Asn-Asn-NHBn are found exclusively in a single conformation in which the peptide backbone engages in a type I ß-turn with its C10 H-bond. The Asn residue(s) stabilize this ß-turn via C6 H-bond(s) between the carboxamide C═O group and the same residue's amide NH. These structures are closely analogous to the corresponding structures in Gln-containing peptides studied previously [Walsh, P. S. et al. PCCP 2016, 18, 11306-11322; Walsh, P. S. et al. Angew. Chem. Int. Ed. 2016, 55, 14618-14622], indicating that the Asn and Gln side chains can each configure so as to stabilize the same backbone conformations. Spectroscopic and computational evidence suggest that glutamine is more predisposed than asparagine to ß-turn formation via unusually strong side-chain-backbone hydrogen-bond formation. Further spectral and structural similarities and differences due to the side-chain length difference of these similar amino acids are presented and discussed.

Infrared Population Transfer Spectroscopy of Cryo-Cooled Ions: Quantitative Tests of the Effects of Collisional Cooling on the Room Temperature Conformer Populations.

The single-conformation spectroscopy and infrared-induced conformational isomerization of a model protonated pentapeptide [YGPAA + H]+ is studied under cryo-cooled conditions in the gas phase. Building on recent results ( DeBlase , A. F. ; J. Am. Chem. Soc. 2017 , 139 , 5481 - 5493 ), firm assignments are established for the presence of two conformer families with distinct infrared and ultraviolet spectra, using IR-UV depletion spectroscopy. Families (A and B) share a similar structure near the N-terminus but differ in the way that the C-terminal COOH group configures itself (cis versus trans) in forming H-bonds with the peptide backbone. Infrared population transfer (IR-PT) spectroscopy is used to study the IR-induced conformational isomerization following single-conformer infrared excitation. IR-induced isomerization is accomplished in both directions (A → B and B → A) in the hydride stretch region and is used to determine fractional abundances for the two conformer families (FA = 0.65 ± 0.04, FB = 0.35 ± 0.04, 2σ error bars). The time scale for collisional cooling of the room-temperature ions to Tvib = 10 K by cold helium in the octupole trap is established as 1.0 ms. Key stationary points on the isomerization potential energy surface are calculated at the DFT B3LYP/6-31+G(d) G3DBJ level of theory. Using RRKM theory, the energy-dependent isomerization rates and populations are calculated as a function of energy. According to the model, the observed population distribution after collisional cooling is close to that of the 298 K Boltzmann distribution and is in near-quantitative agreement with experiment. On the basis of this success, inferences are drawn for the circumstances that govern the population distribution in the trap, concluding that, in ions the size of [YGPAA + H]+ and larger, the observed distributions will be near those at 298 K.