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Correction for 'Single-conformation spectroscopy of cold, protonated DPG-containing peptides: switching ß-turn types and formation of a sequential type II/II' double ß-turn' by John T. Lawler et al., Phys. Chem. Chem. Phys., 2022, 24, 2095-2109, https://doi.org/10.1039/D1CP04852J.

RESUMEN

D-Proline (DPro, DP) is widely utilized to form ß-hairpin loops in engineered peptides that would otherwise be unstructured, most often as part of a DPG sub-unit that forms a ß-turn. To observe whether DPG facilitated this effect in short protonated peptides, conformation specific IR-UV double resonance photofragment spectra of the cold (∼10 K) protonated DP and LP diastereomers of the pentapeptide YAPGA was carried out in the hydride stretch (2800-3700 cm-1) and amide I/II (1400-1800 cm-1) regions. A model localized Hamiltonian was developed to better describe the 1600-1800 cm-1 region commonly associated with the amide I vibrations. The CO stretch fundamentals experience extensive mixing with the N-H bending fundamentals of the NH3+ group in these protonated peptides. The model Hamiltonian accounts for experiment in quantitative detail. In the DP diastereomer, all the population is funneled into a single conformer which presented as a type II ß-turn with A and DP in the i + 1 and i + 2 positions, respectively. This structure was not the anticipated type II' ß-turn across DPG that we had hypothesized based on solution-phase propensities. Analysis of the conformational energy landscape shows that both steric and charge-induced effects play a role in the preferred formation of the type II ß-turn. In contrast, the LP isomer forms three conformations with very different structures, none of which were type II/II' ß-turns, confirming that LPG is not a ß-turn former. Finally, single-conformation spectroscopy was also carried out on the extended peptide [YAADPGAAA + H]+ to determine whether moving the protonated N-terminus further from DPG would lead to ß-hairpin formation. Despite funneling its entire population into a single peptide backbone structure, the assigned structure is not a ß-hairpin, but a concatenated type II/type II' double ß-turn that displaces the peptide backbone laterally by about 7.5 Å, but leaves the backbone oriented in its original direction.

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Two-color infrared multiphoton dissociation (2C-IRMPD) spectroscopy is a technique that mitigates spectral distortions due to nonlinear absorption that is inherent to one-color IRMPD. We use a 2C-IRMPD scheme that incorporates two independently tunable IR sources, providing considerable control over the internal energy content and type of spectrum obtained by varying the trap temperature, the time delays and fluences of the two infrared lasers, and whether the first or second laser wavelength is scanned. In this work, we describe the application of this variant of 2C-IRMPD to conformationally complex peptide ions. The 2C-IRMPD technique is used to record near-linear action spectra of both cations and anions with temperatures ranging from 10 to 300 K. We also determine the conditions under which it is possible to record IR spectra of single conformers in a conformational mixture. Furthermore, we demonstrate the capability of the technique to explore conformational unfolding by recording IR spectra with widely varying internal energy in the ion. The protonated peptide ions YGGFL (NH3+-Tyr-Gly-Gly-Phe-Leu, Leu-enkephalin) and YGPAA (NH3+-Tyr-Gly-Pro-Ala-Ala) are used as model systems for exploring the advantages and disadvantages of the method when applied to conformationally complex ions.

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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.

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Gas-phase ion chemistry methods that capture and characterize the degree of activation of small molecules in the active sites of homogeneous catalysts form a powerful new tool to unravel how ligand environments affect reactivity. A key roadblock in this development, however, is the ability to generate the fragile metal oxidation states that are essential for catalytic activity. Here we demonstrate the preparation of the key Ni(I) center in the widely used cyclam scaffold using ion-ion recombination as a gas-phase alternative to electrochemical reduction. The singly charged Ni+(cyclam) coordination complex is generated by electron transfer from fluoranthene and azobenzene anions to doubly charged Ni2+(cyclam), using the electron-transfer dissociation protocol in a commercial quadrupole ion trap instrument and in a custom-built octopole RF ion trap. The successful preparation of the Ni+(cyclam) cation is verified through analysis of its vibrational spectrum obtained using the infrared free electron laser FELIX.

RESUMEN

Incorporation of the unnatural d-proline (DP) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of ß-hairpin loops because natural sequences are often unstructured in solution. Using conformation-specific IR and UV spectroscopy of cold (≈10 K) gas-phase ions, we probe the inherent conformational preferences of the DP and LP diastereomers in the protonated peptide [YAPAA+H]+, where only intramolecular interactions are possible. Consistent with the solution-phase studies, one of the conformers of [YADPAA+H]+ is folded into a charge-stabilized ß-hairpin turn. However, a second predominant conformer family containing two sequential γ-turns is also identified, with similar energetic stability. A single conformational isomer of the LP diastereomer, [YALPAA+H]+, is found and assigned to a structure that is not the anticipated "mirror image" ß-turn. Instead, the LP stereocenter promotes a cis-alanine-proline amide bond. The assigned structures contain clues that the preference of the DP diastereomer to support a trans-amide bond and the proclivity of LP for a cis-amide bond is sterically driven and can be reversed by substituting glycine for alanine in position 2, forming [YGLPAA+H]+. These results provide a basis for understanding the residue-specific and stereospecific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of ß-hairpin formation.

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We employ cold ion spectroscopy (UV action and IR-UV double resonance) in the gas phase to unravel the qualitative structural elements of G-type alkali metal cationized (X = Li(+), Na(+), K(+)) tetralignol complexes connected by ß-O-4 linkages. The conformation-specific spectroscopy reveals a variety of conformers, each containing distinct infrared spectra in the OH stretching region, building on recent studies of the neutral and alkali metal cationized ß-O-4 dimers. The alkali metal ion is discovered to bind in penta-coordinate pockets to ether and OH groups involving at least two of the three ß-O-4 linkages. Different binding sites are distinguished from one another by the number of M(+)···OH···O interactions present in the binding pocket, leading to characteristic IR transitions appearing below 3550 cm(-1). This interaction is mitigated in the major conformer of the K(+) adduct, demonstrating a clear impact of the size of the charge center on the three-dimensional structure of the tetramer.

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Ultraviolet and infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy has been carried out in a tandem mass spectrometer to determine the three-dimensional structure of cryogenically cooled protonated C-terminally methyl esterified leucine enkephalin [YGGFL-OMe+H](+). By comparing the experimental IR spectrum of the dominant conformer with the predictions of DFT M05-2X/6-31+G(d) calculations, a backbone structure was assigned that is analogous to that previously assigned by our group for the unmodified peptide [ Burke, N.L.; et al. Int. J. Mass Spectrom. 2015 , 378 , 196 ], despite the loss of a C-terminal OH binding site that was thought to play an important role in its stabilization. Both structures are characterized by a type II' ß-turn around Gly(3)-Phe(4) and a γ-turn around Gly(2), providing spectroscopic evidence for the formation of a ß-hairpin hydrogen bonding pattern. Rather than disrupting the peptide backbone structure, the protonated N-terminus serves to stabilize the ß-hairpin by positioning itself in a pocket above the turn where it can form H-bonds to the Gly(3) and C-terminus C═O groups. This ß-hairpin type structure has been previously proposed as the biologically active conformation of leucine enkephalin and its methyl ester in the nonpolar cell membrane environment [ Naito, A.; Nishimura, K. Curr. Top. Med. Chem. 2004 , 4 , 135 - 143 ].

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To understand how the D2d oxalate scaffold (C2O4)(2-) distorts upon capture of a proton, we report the vibrational spectra of the cryogenically cooled HO2CCO2(-) anion and its deuterated isotopologue DO2CCO2(-). The transitions associated with the skeletal vibrations and OH bending modes are sharp and are well described by inclusion of cubic terms in the normal mode expansion of the potential surface through an extended Fermi resonance analysis. The ground state structure features a five-membered ring with an asymmetric intramolecular proton bond. The spectral signatures of the hydrogen stretches, on the contrary, are surprisingly diffuse, and this behavior is not anticipated by the extended Fermi scheme. We trace the diffuse bands to very strong couplings between the high-frequency OH-stretch and the low-frequency COH bends as well as heavy particle skeletal deformations. A simple vibrationally adiabatic model recovers this breadth of oscillator strength as a 0 K analogue of the motional broadening commonly used to explain the diffuse spectra of H-bonded systems at elevated temperatures, but where these displacements arise from the configurations present at the vibrational zero-point level.

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The role of proton-assisted charge accommodation in electron capture by a heterocyclic electron scavenger is investigated through theoretical analysis of the vibrational spectra of cold, gas phase [Py ⋅ (H2O)n=3-5](-) clusters. These radical anions are formed when an excess electron is attached to water clusters containing a single pyridine (Py) molecule in a supersonic jet ion source. Under these conditions, the cluster ion distribution starts promptly at n = 3, and the photoelectron spectra, combined with vibrational predissociation spectra of the Ar-tagged anions, establish that for n > 3, these species are best described as hydrated hydroxide ions with the neutral pyridinium radical, PyH((0)), occupying one of the primary solvation sites of the OH(-). The n = 3 cluster appears to be a special case where charge localization on Py and hydroxide is nearly isoenergetic, and the nature of this species is explored with ab initio molecular dynamics calculations of the trajectories that start from metastable arrangements of the anion based on a diffuse, essentially dipole-bound electron. These calculations indicate that the reaction proceeds via a relatively slow rearrangement of the water network to create a favorable hydration configuration around the water molecule that eventually donates a proton to the Py nitrogen atom to yield the product hydroxide ion. The correlation between the degree of excess charge localization and the evolving shape of the water network revealed by this approach thus provides a microscopic picture of the "solvent coordinate" at the heart of a prototypical proton-coupled electron transfer reaction.

RESUMEN

The gas phase structure of deprotonated cysteine (Cys-H(+))(-) has recently gained attention because of its counterintuitive calculated minimum energy structure in which it appears that deprotonation occurs at the -SH moiety rather than at the nominally more acidic carboxylic acid group. Because previous experimental efforts have not yielded to a consensus regarding the structure of the anion, we report the cryogenic ion vibrational predissociation (CIVP) spectra of its cryogenically cooled H/D isotopologues in an effort to clarify the situation. The unexpected isotope dependence of key features in the spectrum and the similarity of the band pattern to that displayed by the intramolecular H-bonded linkage in a deprotonated diacid (HCO2(CH2)10CO2(-)) indicate that the dominant form of the anion occurs with a strongly shared proton between the thiolate (-S(-)) and carboxylate (-CO2(-)) groups. An interesting aspect of this (-S(-)···H(+)···(-)O2C-) linkage is that, although the global minimum places the shared proton closer to the oxygen atom, the soft potential energy curve calculated for displacement of the bridging proton would likely support sufficient zero-point motion both to blur the distinction between thiolate- and carboxylate-based structures and to account for the unusual isotope effects.

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We analyze the structures and spectral signatures of the cyclic intramolecular proton bond, N-H(+)-A, A = O and F, formed when an excess proton is added to derivatives of the 1,8-disubstituted naphthalene scaffold. These compounds provide a quasi-rigid framework with which to study the spectral complexity often associated with the N-H(+)-A entity. Vibrational spectra were obtained by monitoring photodissociation of weakly bound H2 adducts of the mass-selected ions cooled close to 10 K. Several bands across the 900-3500 cm(-1) spectral range were traced to involvement of the bridging proton by their telltale shifts upon selective H∕D isotopic substitution at that position. We account for the complex patterns that occur near the expected locations of the NH stretching fundamentals in the context of background levels mixing with a "bright" zero-order state through cubic terms in the potential energy expansion. Thus, this system provides a detailed picture of one of the mechanisms behind the line broadening often displayed by embedded excess protons. It does so in a sufficiently sparse density of states regime that many discrete transitions are observed in the vicinity of the harmonic stretching transition involving displacement of the trapped proton.

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The (HCOOH)(2) anion, formed by electron attachment to the formic acid dimer (FA(2)), is an archetypal system for exploring the mechanics of the electron-induced proton transfer motif that is purported to occur when neutral nucleic acid base-pairs accommodate an excess electron [K. Aflatooni, G. A. Gallup, and P. D. Burrow, J. Phys. Chem. A 102, 6205 (1998); J. H. Hendricks, S. A. Lyapustina, H. L. de Clercq, J. T. Snodgrass, and K. H. Bowen, J. Chem Phys. 104, 7788 (1996); C. Desfrancois, H. Abdoul-Carime, and J. P. Schermann, ibid. 104, 7792 (1996)]. The FA(2) anion and several of its H∕D isotopologues were isolated in the gas phase and characterized using Ar-tagged vibrational predissociation and electron autodetachment spectroscopies. The photoelectron spectrum of the FA(2) anion was also recorded using velocity-map imaging. The resulting spectroscopic information verifies the equilibrium FA(2)(-) geometry predicted by theory which features a symmetrical, double H-bonded bridge effectively linking together constituents that most closely resemble the formate ion and a dihydroxymethyl radical. The spectroscopic signatures of this ion were analyzed with the aid of calculated anharmonic vibrational band patterns.

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We characterize a highly unusual, charged NH-O hydrogen bond formed within esters of 8-(dimethylamino)naphthalen-1-ol in which an ammonium ion serves as an intramolecular hydrogen bond donor to spatially proximate ester ether oxygen atoms. Infrared spectroscopic analysis of the ester carbonyl frequencies demonstrates significant blue-shifting when ether hydrogen bonding is possible, in stark contrast to the more commonly observed red shift that occurs upon hydrogen bonding to the ester carbonyl oxygen. The intrinsic behavior of the linkage (i.e., in which counterions and solvent effects are eliminated) is provided by vibrational predissociation spectroscopy of the isolated gas-phase cations complexed with weakly bound D(2) molecules.

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The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive "hydrated electron" onto a neutral CO(2) molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO(2) or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO(2)·(H(2)O)(6)(-) clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.

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We report detailed studies on the characterization of an intramolecular NH-F hydrogen bond formed within a fluorinated "proton sponge" derivative. An ammonium ion, generated from 8-fluoro-N,N-dimethylnaphthalen-1-amine, serves as a charged hydrogen bond donor to a covalently bound fluorine appropriately positioned on the naphthalene skeleton. Potentiometric titrations of various N,N-dimethylnaphthalen-1-amines demonstrate a significant increase in basicity when hydrogen bonding is possible. X-ray crystallography reveals that NH-F hydrogen bonding in protonated 8-fluoro-N,N-dimethylnaphthalen-1-amine is heavily influenced by ion pairing in the solid state; bifurcated and trifurcated hydrogen bonds are formed depending on the counterion utilized. Compelling evidence of hydrogen bonding in the 8-fluoro-N,N-dimethylnaphthyl-1-ammonium cation is provided by gas-phase cryogenic vibrational photodissociation spectroscopy. Solution-phase infrared spectroscopy provides complementary results, and the frequencies of the N-H stretching mode in both phases are in excellent agreement with the computed vibrational spectra. NMR analysis of protonated 8-fluoro-N,N-dimethylnaphthalen-1-amine demonstrates significant H-F coupling between the N-H hydrogen and fluorine that cannot be attributed to long-range, through-bond interactions; the couplings correlate favorably with calculated values. The results obtained from these experiments are congruent with the formation of an NH-F hydrogen bond upon protonation of 8-fluoro-N,N-dimethylnaphthalen-1-amine.

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The main molecule of the title compound, C(37)H(36)·CDCl(3), is a hydro-carbon with two naphthalene segments attached to opposite ends of a rigid norbornylogous spacer with an overall structure that is approximately C-shaped. The dihedral angle between the naphthalene ring planes is 9.27 (7)°. The cleft that exists between the naphthalene rings is large enough that the compound crystallizes with a solvent mol-ecule (CDCl(3)) in the cleft. The CDCl(3) solvent mol-ecule is present in two disordered orientations in a 3:2 ratio, each involving C-D⋯π to C(6) ring centers.