Alkali cation chelation in cold β-o-4 tetralignol complexes

Lignins are the second most abundant naturally occurring polymer class, contributing to about 30\% of the organic carbon in the biosphere. Their primary function is to provide the structural integrity of plant cell walls and have recently come under consideration as a potential source of biofuels because they have an energy content similar to coal. Herein, we employ cold ion spectroscopy (UV action and IR-UV double resonance) to unravel the spectroscopic signatures of G-type alkali metal cationized (X = Li$^{+}$, Na$^{+}$, K$^{+}$) lignin tetramers connected by $\beta$-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 on the neutral and alkali metal cationized $\beta$-O-4 dimers. Based on comparisons of our infrared spectra to density functional theory [M05-2X/6-31+G] harmonic level calculations for structures derived from a Monte Carlo conformational search, the alkali metal ion is discovered to engage in M$^{+}$-OH-O interactions as important motifs that determine the secondary structures of these complexes. This interaction disappears in the major conformer of the K$^{+}$ adduct, suggesting a reemergence of a neutral dimer segment as the metal binding energy decreases. Chelation of the metal cation by oxygen lone pair(s) of nearby oxygens in the $\beta$-O-4 linkage is observed to be the predominant driving force for 3D structure around the charge site, relegating OH-O H-bonds as secondary stabilizing elements

IR-UV double resonance spectroscopy of a cold protonated fibril-forming peptide: NNQQNY·H+

Protein aggregation to form amyloid-like fibrils is a purported molecular manifestation that leads to Alzheimer’s, Huntington’s, and other neurodegenerative diseases. The propensity for a protein to aggregate is often driven by the presence of glutamine (Q) and asparagine (N) rich tracts within the primary sequence. For example, Eisenberg and coworkers [Nature 2006, 435, 773] have shown by X-ray crystallography that the peptides NNQQNY and GNNQQNY aggregate into a parallel $\beta$-sheet configuration with side chains that intercalate into a “steric zipper”. These sequences are commonly found at the N-terminus of the prion-determining domain in the yeast protein Sup35, a typical fibril-forming protein. Herein, we invoke recent advances in cold ion spectroscopy to explore the nascent conformational preferences of the protonated peptides that are generated by electrospray ionization. Towards this aim, we have used UV and IR spectroscopy to record conformation-specific photofragment action spectra of the NNQQNY monomer cryogenically cooled in an octopole ion trap. This short peptide contains 20 hydride stretch oscillators, leading to a rich infrared spectrum with at least 18 resolved transitions in the 2800-3800 cm$^{-1}$ region. The infrared spectrum suggests the presence of both a free acid OH moiety and an H-bonded tyrosine OH group. We compare our results with resonant ion dip infrared spectra (RIDIRS) of the acyl/NH-benzyl capped neutral glutamine amino acid and its corresponding dipeptide: Ac-Q-NHBn and Ac-QQ-NHBn, respectively. These comparisons bring empirical insight to the NH stretching region of the spectrum, which contains contributions from free and singly H-bonded NH$_{2}$ side-chain groups, and from peptide backbone amide NH groups. We further compare our spectrum to harmonic calculations at the M05-2X/6-31+G level of theory, which were performed on low energy structures obtained from Monte Carlo conformational searches using the Amber and OPLS force fields to assess the presence of sidechain-sidechain and sidechain-backbone interactions

CONFORMATION-SPECIFIC INFRARED AND ULTRAVIOLET SPECTROSCOPY OF COLD [YAPAA+H]+ AND [YGPAA+H]+ IONS: A STEREOCHEMICAL 'TWIST' ON THE β-HAIRPIN TURN

Incorporation of the unnatural D-proline ($^{D}$P) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of $beta$-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 $^{D}$P and $^{L}$P 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 $beta$-hairpin turn. However, a second predominant conformer family containing two sequential $gamma$-turns is also identified, with similar energetic stability. A single conformational isomer of the $^{L}$P diastereomer, [YALPAA+H]$^{+}$, is found and assigned to a structure that is not the anticipated “mirror image” $beta$-turn. Instead, the $^{L}$P stereo center promotes a cis alanine-proline amide bond. The assigned structures contain clues that the preference of the $^{D}$P diastereomer to support a trans-amide bond and the proclivity of $^{L}$P 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 stereo-specific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of $beta$-hairpin formation

WATER-NETWORK MEDIATED, ELECTRON INDUCED PROTON TRANSFER IN ANIONIC [C5H5N·(H2O)n]− CLUSTERS: SIZE DEPENDENT FORMATION OF THE PYRIDINIUM RADICAL FOR n ≥ 3

As an isolated species, the radical anion of pyridine (Py$^{-}$) exists as an unstable transient negative ion, while in aqueous environments it is known to undergo rapid protonation to form the neutral pyridinium radical [PyH$^{(0)}$] along with hydroxide. Furthermore, the negative adiabatic electron affinity (AEA) of Py$^{-}$ can become diminished by the solvation energy associated with cluster formation. In this work, we focus on the hydrates [Py$cdot$(H$_{2}$O)$_{n}$]$^{-}$ with n = 3-5 and elucidate the structures of these water clusters using a combination of vibrational predissociation and photoelectron spectroscopies. We show that H-trasfer to form PyH$^{(0)}$ occurs in these clusters by the infrared signature of the nascent hydroxide ion and by the sharp bending vibrations of aromatic ring CH bending

syn,syn-15,17-Di-2-naphthyl­hexa­cyclo­[10.2.1.13,10.15,8.02,11.04,9]hepta­decane deuterochloro­form monosolvate

The main molecule of the title compound, C37H36·CDCl3, is a hydro­carbon 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 mol­ecule (CDCl3) in the cleft. The CDCl3 solvent mol­ecule is present in two disordered orientations in a 3:2 ratio, each involving C—D⋯π to C 6 ring centers

SPECTROSCOPIC INVESTIGATION OF ELECTRON-INDUCED PROTON TRANSFER IN THE FORMIC ACID DIMER, (HCOOH)2_{2}

Author Institution: Yale University, Department of Chemistry, New Haven, CTWe have isolated the stable form of the formic acid dimer anion (HCOOH)$_{2}^{-}$, a model for electron-induced proton transfer between nucleic acid base-pairs, in the gas phase. The vibrational signatures of this species and its various isotopomers were investigated using Ar predissociation and photodetachment spectroscopies in the 600-3800 \wn\ range. We relate the experimental infrared transitions of the anion to those predicted for its calculated lowest energy structure in order to determine if a proton transfer event does in fact occur upon excess electron attachment to this simple hydrogen-bonded dimer. Additionally, we determined its vertical detachment energy (VDE), 1.8 eV, using velocity-map photoelectron imaging

USING AN ORGANIC SCAFFOLD TO MODULATE THE QUANTUM STRUCTURE OF AN INTRAMOLECULAR PROTON BOND: CRYOGENIC VIBRATIONAL PREDISSOCIATION SPECTROSCOPY OF H2_{2} ON PROTONATED 8-NAPHTHALENE-1-AMINE

Author Institution: Sterling Chemistry, Yale University, New Haven, Ct, 06520; DEPARTMENT OF CHEMISTRY, JOHNS HOPKINS UNIVERSITY, 3400 NORTH CHARLES STREET, BALTIMORE, MD, 21218The quantum structure of the intermolecular proton bond is a key aspect in understanding proton transfer events that govern the efficiency of fuel cells and various biological membranes. Previously, we have constructed a soft binding motif, that consists of a "point contact" between the lone pairs of two small molecules (combinations of ethers, alcohols, ammonia, and water) that are linked by a shared proton [\textit{Science} 2007, \textit{613}, 249]. Although the frequency of the shared proton vibration has been correlated with effects of acid and base structure, such as proton affinities and dipole moments, the spatial arrangement of the proton donor and acceptor remains unexplored. Towards this aim, we have obtained a molecule of rigid topology that contains a proton donor and acceptor capable of intramolecular proton-bonding (protonated 8-flouronaphthalene-1-amine). Using electrospray ionization coupled with a novel cryogenic mass spectrometry scheme, we employ vibrational predissociation spectroscopy of H$_{2}$ tagged ions to elucidate how a forced spatial configuration of the acid and base perturbs the energetics of the proton bond

"PROTON SPONGES": A RIGID ORGANIC SCAFFOLD TO REVEAL THE QUANTUM STRUCTURE OF THE INTRAMOLECULAR PROTON BOND

Author Institution: Yale University, P. O. Box 208107, New Haven, CT, 06520; Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218; Brock University, St. Catherines, ON, Canada L2S 3A1Spectroscopic analysis of systems containing charged hydrogen bonds (e.g. the Zundel ion, $\mathrm{H}_{5}\mathrm{O}_{2}^{+}$) in a vibrationally cold regime is useful in decongesting numerous anharmonic features common to room temperature measurements.[Roscioli, J. R.; et. al. Science 2007] This approach has been extended to conjugate acids of the "Proton Sponge" family of organic compounds, which contain strong intramolecular hydrogen bonds between proton donor (D) and acceptor (A) groups at the 1- and 8-positions. By performing $\mathrm{H}_2/\mathrm{D}_2$ vibrational predissociation spectroscopy on cryogenically cooled ions, we explore how the proximity and spatial orientation of D and A moieties relates to the spectroscopic signature of the shared proton. In the cases studied ($\mathrm{D = Me_{2}N-H^{+}; A = OH, O(C=O)Ph}$), we observe strong anharmonic couplings between the shared proton and dark states that persist at these cryogenic temperatures. This leads to intense NH stretching features throughout the nominal CH stretching region ($2800-3000 \mathrm{cm}^{-1}$). Isotopic substitution has verified that the oscillator strength of these broad features is driven by NH stretching. Furthermore, the study of A = O(C=O)Ph has provided a spectroscopic snapshot of the shared proton at work as an active catalytic moiety fostering ester hydrolysis by first order acylium fission ($\mathrm{A_{AC}1}$). This is apparent by the high frequency carbonyl stretch at $1792\ \mathrm{cm}^{-1}$, which is a consequence of the strong hydrogen bond to the ether-ester oxygen atom. Thus, these "Proton Sponges" are useful model systems that unearth the quantum structure and reactivity of shared proton interactions in organic compounds