Resonant Ion-dip Infrared Spectroscopy Research Articles

Mixed 14/16 Helices in the Gas Phase: Conformation-Specific Spectroscopy of Z-(Gly)n,n= 1, 3, 5

Single-conformation ultraviolet and infrared spectroscopy has been carried out on the neutral peptide series, Z-(Gly)(n)-OH, n = 1,3,5 (ZGn) and Z-(Gly)(5)-NHMe (ZG5-NHMe) in the isolated environment of a supersonic expansion. The N-terminal Z-cap (carboxybenzyl) provides an ultraviolet chromophore for resonant two-photon ionization (R2PI) spectroscopy. Conformation-specific infrared spectra were recorded in double resonance using resonant ion-dip infrared spectroscopy (RIDIRS). By comparing the experimental spectra with the predictions of DFT M05-2X/6-31+G(d) calculations, the structures could be characterized in terms of the sequence of intramolecular H-bonded rings of varying size. Despite the enhanced flexibility of the glycine residues, a total of only six conformers were observed among the four molecules. Two conformers for ZG1 were found with the major conformation taking on an extended, planar β-strand conformation. Two conformers were observed for ZG3, with the majority of the population in a C11/C7/C7/π(g-) structure that forms a full loop of the glycine chain. Both ZG5 molecules had their population primarily in a single conformation, with structures characteristic of the first stages of a "mixed" β-helix. C14/C16 H-bonded rings in opposing directions (N → C and C → N) tie the helix together, with nearest-neighbor C7 rings turning the backbone so that it forms the helix. φ/ψ angles alternate in sign along the backbone, as is characteristic of the mixed, C14/C16 β-helix. The calculated conformational energies of these structures are unusually stable relative to all others, with energies significantly lower than the PGI/PGII conformations characteristic of polyglycine structures in solution and in the crystalline form, where intermolecular H-bonds play a role.

Competition between Amide Stacking and Intramolecular H Bonds in γ-Peptide Derivatives: Controlling Nearest-Neighbor Preferences

Resonant two-photon ionization (R2PI), IR-UV holeburning (IR-UV), and resonant ion-dip infrared spectroscopy (RIDIRS) have been used to record mass-selected, single-conformation ultraviolet and infrared spectra of three simple diamide derivatives of γ-amino acids as isolated molecules cooled in a supersonic expansion. This work builds on an earlier study of Ac-γ(2)-hPhe-NHMe (James, W. H., III, et al. J. Am. Chem. Soc. 2009, 131, 14243), which showed that this methyl-capped γ-peptide forms amide-stacked conformations that are similar in stability to H-bonded conformations containing a C9 ring and more stable than C7 H-bonded ring structures. Among the γ-peptides discussed here, Ac-γ(2)-hPhe-N(Me)(2) contains an additional methyl group relative to the previously studied Ac-γ(2)-hPhe-NHMe and therefore lacks the amide NH group responsible for C9 ring formation. Three conformations of Ac-γ(2)-hPhe-N(Me)(2) are observed, all of which are amide-stacked structures. In a second new molecule, Ac-γ(2)-hPhe-NH(iPr), the C-terminal NHMe group of Ac-γ(2)-hPhe-NHMe is replaced with an NH(iPr) group. Three conformations of Ac-γ(2)-hPhe-NH(iPr) are observed, all of which are C9 H-bonded structures. The dramatic difference between C-terminal NHMe and NH(iPr) reveals the delicate balance of noncovalent forces within these γ-peptides. The third molecule we examined is a gabapentin-derived diamide (designated 1), which contains a phenylacyl group at the N-terminus and an N(Me)(2) group at the C-terminus; the latter precludes C9 H bonding. Comparison of 1 with Ac-γ(2)-hPhe-N(Me)(2) allows us to examine the impact of the backbone substitution pattern (monosubstitution at carbon-2 vs disubstitution at carbon-3) on the competition between the C7 H-bonded and the amide-stacked conformation. In this case, only C7 rings are observed. The different gas-phase behaviors observed among the molecules analyzed here offer insight on the intrinsic conformational propensities of the γ-peptide backbone, information that provides a foundation for future foldamer design efforts.

Nature of the N−H···S Hydrogen Bond

The N-H...S hydrogen-bonded complexes of the model compounds of tryptophan (indole and 3-methylindole) and methionine (dimethyl sulfide, Me(2)S) have been characterized by a combination of experimental techniques like resonant two-photon ionization (R2PI), resonant ion dip infrared spectroscopy (RIDIRS), and fluorescence dip infrared spectroscopy (FDIRS) and computational methods like ab initio electronic structure calculations, atoms-in-molecules (AIM), natural bond orbital (NBO), and energy decomposition analyses. The results are compared with the N-H...O (M.H(2)O; M = indole, 3-methyl indole) sigma-type and N-H...Phi (M.benzene) pi-type hydrogen-bonded complexes. It was shown that the S(1)-S(0) band origin red shifts in the N-H...S hydrogen-bonded complexes correlated well with the polarizability of the acceptor rather than their proton affinity, contrary to the trend observed in most X-H...Y (X, Y = O, N, halogens, etc.) hydrogen-bonded systems. The red shift in the N-H stretching frequency in the N-H...S HB clusters (Me(2)S as HB acceptor) was found to be 1.8 times greater than that for the N-H...O hydrogen-bonded complexes (H(2)O as HB acceptor), although the binding energies for the two complexes were comparable. The energy decomposition analyses for all of the N-H...S hydrogen-bonded complexes showed that the correlation (or dispersion) energy has significant contribution to the total binding energy. It is pointed out that the binding energy of the N-H...S complex was also comparable to that of the indole.benzene complex, which is completely dominated by the dispersion interaction. Atoms-in-molcules (AIM) and natural bond orbital (NBO) analyses indicated a nontrivial electrostatic component in the hydrogen-bonding interaction. Greater dispersion contribution to the stabilization energy as well as greater red shifts in the N-H stretch relative to those of N-H...O hydrogen-bonded complexes makes the indole.dimethylsulfide complex unique in regard to the simultaneous influence of both the dispersion and electrostatic forces. For the sake of comparison, it is pointed out that the red shifts in the O-H stretch for O-H...S and O-H...O hydrogen-bonded complexes were almost the same in the case of para-cresol.Me(2)S and para-cresol.H(2)O complexes ( J. Chem. Phys. 2008 , 128 , 184311. and J. Phys. Chem. A 2009 , 113 , 5633 - 5643 ). This suggests that the strength of the N-H...S hydrogen bonding is stronger than the N-H...O hydrogen bonding. The N-H...S hydrogen bonding was observed for the first time using jet-cooled conditions, and the most interesting feature of this study is that N-H...S "sigma-type" hydrogen bonding behaves more like C-H...Phi or N-H...Phi "pi-type" hydrogen bonding in regard to the dispersion domination in the total interaction energy.

Isomer-Specific Spectroscopy and Conformational Isomerization Energetics of o-, m-, and p-Ethynylstyrenes

The infrared and ultraviolet spectroscopy of o-, m-, and p-ethynylstyrene isomers (oES, mES, and pES) were studied by a combination of methods, including resonance-enhanced two-photon ionization (R2PI), UV-UV hole-burning spectroscopy (UVHB), resonant ion-dip infrared spectroscopy (RIDIRS), and rotationally resolved fluorescence excitation spectroscopy. In addition, the newly developed method of stimulated emission pumping-population transfer spectroscopy (SEP-PTS) was used to determine the energy threshold to conformational isomerization in m-ethynylstyrene. The S(1) <-- S(0) origin transitions of oES and pES occur at 32 369 and 33 407 cm(-1), respectively. In mES, the cis and trans conformations are calculated to be close in energy. In the R2PI spectrum of mES, the two most prominent peaks (32672 and 32926 cm(-1)) were confirmed by UVHB spectroscopy to be S(1) <-- S(0) origins of these two conformers. The red-shifted conformer was identified as the cis structure by least-squares fitting of the rotationally resolved fluorescence excitation spectrum of the origin band. There are also two possible conformations in oES, but transitions due to only one were observed experimentally, as confirmed by UVHB spectroscopy. Density functional theory calculations (B3LYP/6-31+G) predict that the cis-ortho conformer, in which the substituents point toward each other, is about 8 kJ/mol higher in energy than the trans-ortho isomer, and should only be about 5% of the room temperature population of oES. Ground-state infrared spectra in the C-H stretch region (3000-3300 cm(-1)) of each isomer were obtained with RIDIRS. In all three structural isomers, the acetylenic C-H stretch fundamental was split by Fermi resonance. Infrared spectra were also recorded in the excited electronic state, using a UV-IR-UV version of RIDIR spectroscopy. In all three isomers the acetylenic C-H stretch fundamental was unshifted from the ground state, but no Fermi resonance was seen. The first observed and last unobserved transitions in the SEP-PT spectrum were used to place lower and upper bounds on the barrier to cis --> trans isomerization in m-ethynylstyrene of 990-1070 cm(-1). Arguments are given for the lack of a kinetic shift in the measurement. The analogous trans --> cis barrier is in the same range (989-1065 cm(-1)), indicating that the relative energies of the zero-point levels of the two isomers are (E(ZPL)(cis) - E(ZPL)(trans))= -75 to +81 cm(-1). Both the barrier heights and relative energies of the minima are close to those determined by DFT (Becke3LYP/6-31+G) calculations.

The Spectroscopic Consequences of C−H···π H-Bonding: C6H6−(C4H2)n Clusters with n = 1 and 2

The ultraviolet and infrared spectra of the C6H6−(C4H2)n complexes with n = 1 and 2 have been formed and studied in a supersonic expansion using resonant two-photon ionization (R2PI), resonant ion-dip infrared spectroscopy (RIDIRS), and IR−UV hole-burning spectroscopy. A T-shaped structure is deduced for the complex, with the C4H2 centered, end on, over the benzene ring. This C−H···π H-bond shifts the frequency of the vibronic transitions of C6H6 by 161 cm-1 to the blue. The acetylenic CH stretch fundamental of C4H2 is localized and split by formation of the π H-bond. The H-bonded CH stretch fundamental is lowered in frequency by about 40 cm-1, increased in intensity by more than a factor of 2, and split by a Fermi resonance that is turned on by the complexation. The C6H6−(C4H2)2 complex has a structure that makes the S1−S0 origin transition weakly allowed and possesses an infrared spectrum that has acetylenic CH stretch absorptions due to free CH, aromatic π-bound CH, and a more weakly π-bound CH. Its structure is tentatively assigned as a cyclic, “pinwheel” structure.

Infrared and Ultraviolet Spectroscopy of Jet-Cooled ortho-, meta-, and para-Diethynylbenzene

The vibronic spectroscopy of ortho-, meta-, and para-diethynylbenzene (oDEB, mDEB, and pDEB) was studied by two-color resonant two photon ionization (R2PI). The symmetry allowed S0−S1 origins of oDEB, mDEB, and pDEB were located at 33 515, 33 806, and 34 255 cm-1, respectively, with the vibronic structure extending about 2000 cm-1 above the origin in oDEB and mDEB, but more than 3000 cm-1 in pDEB. Major peaks in each spectrum were attributed to vibronically induced bands, indicating strong coupling of the S1 state to the S2 state. Ground-state infrared spectra in the C−H stretch region (3000−3360 cm-1) were obtained using resonant ion-dip infrared spectroscopy (RIDIRS). In all three isomers, the acetylenic C−H stretch fundamental was split by Fermi resonance with a combination band composed of the C⋮C stretch and two quanta of the C⋮CH bend. This Fermi resonance was detuned in the overtone region of pDEB, which showed a single peak at 6556 cm-1. Infrared spectra were also recorded in the excited electroni...

Sugars in the gas phase

The gas-phase conformation of the model glycoside, phenyl β-D-galactopyranoside (phe-β-D-gal) was examined using a combination of resonant two-photon ionization (R2PI) and resonant ion-dip infrared spectroscopy (RIDIRS) in tandem with electronic structure theory calculations. A single conformer, in which the hydroxy methyl is in a gauche+ orientation, is predominant in the free-jet expansion. This conformer is the analogue of the lowest-energy conformer found in a previous study of phenyl β-D-glucopyranoside. A minor second conformer has also been identified. Other weak bands in the R2PI spectrum have been attributed to hot bands though it is possible that other conformers are also present at low abundance. The dominant conformer identified in this work has the same (gauche+) orientation of the hydroxy methyl group as the major rotamer identified in solution by NMR spectroscopy.

Solvation of a Flexible Biomolecule in the Gas Phase: The Ultraviolet and Infrared Spectroscopy of Melatonin−Water Clusters

The neural hormone melatonin (N-acetyl-5-methoxytryptamine) is an indole derivative with a flexible peptide-like side chain that presents five distinct hydrogen-bonding sites for water: the carbonyl oxygen, the amide NH, the indole NH, the methoxy oxygen, and the indole π cloud. Using a combination of two-color resonant two-photon ionization (2C-R2PI), UV−UV hole-burning spectroscopy, and resonant ion-dip infrared spectroscopy (RIDIRS), the conformational preferences of melatonin upon sequential solvation with water have been examined. Density functional theory calculations are used to identify structural minima and to aid in the infrared spectral assignments. This work builds on previous results on the melatonin monomer (Florio et al. J. Am. Chem. Soc. 2002, 124, 10236), which identified five monomer conformations: three dominant trans-amide conformers and two minor cis-amide conformers. Four distinct melatonin−(water)1 complexes and two melatonin−(water)2 clusters are observed. All of these feature water binding to the carbonyl group as the primary point of attachment. The dominant two MEL−(water)1 complexes retain the structures of the lowest energy monomer conformations, MEL(A, B). The other two structures (MEL−(water)1 Y and Z) have water bound at the carbonyl group, but also perturb the indole NH stretch fundamental, suggesting that the water molecule interacts with both sites simultaneously. The infrared spectra of the two MEL−(water)2 clusters point to a bridge structure joining the amide carbonyl and indole NH groups. The changes that occur in the potential energy landscape of melatonin in the presence of water will be discussed.

Conformational preferences of jet-cooled melatonin: probing trans- and cis-amide regions of the potential energy surface.

The hormone melatonin (N-acetyl-5-methoxytryptamine) is an indole derivative with a flexible peptide-like side chain attached at the C3 position. Using a combination of two-color resonant two-photon ionization (2C-R2PI), laser-induced fluorescence excitation (LIF), resonant ion-dip infrared spectroscopy (RIDIRS), fluorescence-dip infrared spectroscopy (FDIRS), and UV-UV hole-burning spectroscopy, the conformational preferences of melatonin in a molecular beam have been determined. Three major trans-amide conformers and two minor cis-amide conformers have been identified in the R2PI spectrum and characterized with RIDIRS and FDIRS. Structural assignments are made using the infrared spectra in concert with density functional theory and localized MP2 calculations. Observation of cis-amide melatonin conformers in the molecular beam, despite the large energy gap (approximately 3 kcal/mol) between trans- and cis-amides, is striking because there are at least nine lower-energy trans-amide minima that are not detected. The implications of this observation for cooling and trapping conformational population in a supersonic expansion are discussed.

Conformation, structure and molecular solvation: a spectroscopic and computational study of 2-phenoxy ethanol and its singly and multiply hydrated clusters

The conformational landscapes of 2-phenoxy ethanol (POX) and its hydrated clusters have been studied in the gas-phase, providing a model for pharmaceutical β-blockers. A combination of experimental techniques, including resonant two-photon ionisation (R2PI), laser-induced-fluorescence (LIF) and resonant ion-dip infra-red spectroscopy (RIDIRS), coupled with high-level ab initio calculations has allowed the assignment of the individually resolved spectral features to discrete conformational and supra-molecular structures. Assignments were made by comparison of experimental vibrational spectra and partially resolved ultra-violet rotational band contours with those predicted from quantum chemical calculations. The isolated molecule displays a solitary structure with an extended geometry of the side-chain which is stabilised by an intramolecular hydrogen-bond between the alcohol (proton donor) and the ether (proton acceptor) groups of the side-chain. In singly hydrated clusters the water molecule is accommodated by insertion into the intramolecular hydrogen-bond. In the doubly hydrated and higher clusters cyclic structures are generated which incorporate both the water molecules and the terminal OH group of the side-chain; additional (weak) hydrogen bonded interactions with the phenoxy group provide a degree of selectivity but essentially, the water ‘droplet’ forms on the end of the alcohol side-chain.

Laser Spectroscopy of Jet-Cooled Biomolecules and Their Water-Containing Clusters: Water Bridges and Molecular Conformation

The techniques of laser-induced fluorescence (LIF), resonant two-photon ionization spectroscopy (R2PI), UV−UV hole-burning spectroscopy, fluorescence-dip infrared spectroscopy (FDIRS), and resonant ion-dip infrared spectroscopy (RIDIRS) have been used to study the ultraviolet and infrared spectra of individual conformations of small, flexible biomolecules cooled in a supersonic expansion. The water-containing clusters of these molecules and of other rigid molecules that possess multiple H-bonding sites are considered. The water molecules in many of the solute−(water)n clusters form hydrogen-bonded bridges between donor and acceptor sites on the solute molecule. The infrared spectroscopy of these bridges has been explored in some detail. Water bridges are also formed when one of the H-bonding sites is on a flexible side chain. These bridges have a profound influence on the conformational preferences of the flexible biomolecules.

The infrared spectroscopy of hydrogen-bonded bridges: 2-pyridone-(water)n and 2-hydroxypyridine-(water)n clusters, n=1,2

The water-containing clusters of the two tautomers 2-hydroxypyridine (2HP) and 2-pyridone (2PYR) are studied in the hydride stretch region of the infrared using the techniques of resonant ion-dip infrared spectroscopy (RIDIRS) and fluorescence-dip infrared spectroscopy (FDIRS). The results on 2PYR-(water)n build on previous high-resolution ultraviolet spectroscopy [Held and Pratt, J. Am. Chem. Soc. 115, 9708 (1993)] on the n=1,2 clusters and the infrared depletion spectra of Matsuda et al. [J. Chem. Phys. 110, 8397 (1999)] on the n=1 cluster. The 2PYR-W2 FDIR spectrum reflects the consequences of extending and strengthening the H-bonded bridge between N–H and C=O sites in 2PYR. The spectrum shows evidence of strong coupling along the bridge, both in the form of the hydride stretch normal modes and in the breadth of the observed infrared transitions. RIDIR spectra of the 2HP-Wn clusters are compared with those of 2PYR-Wn in order to assess the spectroscopic consequences of forming the analogous water bridges in the lactim tautomer. Density functional theory calculations are compared with the RIDIR spectra to deduce that the 2HP-Wn clusters are indeed water-containing bridge structures closely analogous to their 2PYR counterparts. The IR spectra of the 2HP-Wn clusters bear a striking resemblance to those of 2PYR-Wn. Potential reasons for the unusual breadth of the bridge XH stretches are discussed.

Infrared and Ultraviolet Spectroscopy of Water-Containing Clusters of Indole, 1-Methylindole, and 3-Methylindole

A combination of resonant two-photon ionization (R2PI), resonant ion-dip infrared spectroscopy (RIDIRS), and infrared−ultraviolet (IR−UV) hole-burning spectroscopy is used to characterize the hydrogen-bonding topologies of indole−(water)1,2, 1-methylindole−(water)1-3, and 3-methylindole−(water)1 clusters formed and cooled in a supersonic expansion. The combination of methods provides a means of disentangling R2PI spectra that contain contributions from more than one species in the same mass channel due either to fragmentation or to the presence of conformational isomers. Density functional theory calculations (DFT Becke3LYP/6-31+G*) of the structures, harmonic vibrational frequencies, and infrared intensities provide a basis for distinguishing which structures are observed experimentally. The clusters studied exhibit a range of solvation structures around indole. In the indole−(water)1 and 3-methylindole−(water)1 complexes, the RIDIR spectra provide a benchmark frequency shift for the N−H···OH2 H-bonds in...

Probing hydrogen bonding in benzene–(water)nclusters using resonant ion–dip IR spectroscopy

Resonant ion–dip infrared spectroscopy (RIDIRS) is used to record clustersize-specific spectra of C6H6–(H2O)n(BWn) clusters with n= 1–7 in the C—H and O—H stretch regions (2900–4000 cm–1). The Fermi triad characteristic of benzene in the C—H stretch region is virtually unchanged by addition of as many as seven water molecules. By contrast, the O—H stretch spectra show a dramatic dependence on cluster size. In C6H6–H2O, the O—H stretch transitions are complicated by additional structure due to internal rotation of H2O in the complex. In C6H6–(H2O)2, the O—H stretch spectrum closely mimics that of the free water dimer. For the n= 3–5 clusters, the spectra can be divided roughly into three categories, due to free O—H (3715 cm–1), π H-bonded O—H (3650 cm–1), and single donor O—H stretches, consistent with a BWn structure composed of a cyclic Wn cluster in which one of the free O—H groups is used in π hydrogen bonding with benzene. At n= 6, the spectra show distinct new transitions in the 3500–3600 cm–1 region. By comparing with the predictions of ab initio calculations of Wn, these new transitions are assigned to double donor O—H stretches associated with the formation of a more compact, ice-like structure in W6. The transformation to double-donating waters continues to develop in BW7, where additional transitions in the double-donor O—H stretch region appear at the expense of free O—H transition intensity.