Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor that causes growth arrest and differentiation of many tumor types and is an approved drug for the treatment of cancer. The chemical structure of SAHA consists of formanilide “head” and a hydroxamic acid “tail” separated by an n-hexyl chain, C6H5NH(C═O)-(CH2)6-(C═O)NHOH. The alkyl chain’s preference for extended structures is in competition with tail-to-head (T-H) or head-to-tail (H-T) hydrogen bonds between the amide and hydroxamic acid groups. Laser desorption was used to bring SAHA into the gas phase and cool it in a supersonic expansion before interrogation with mass-resolved resonant two-photon ionization spectroscopy. Single conformation UV spectra in the S0-S1 region and infrared spectra in the hydride stretch and mid-IR regions were recorded using IR-UV hole-burning and resonant ion-dip infrared spectroscopy, respectively. Three conformers of SAHA were distinguished and spectroscopically characterized. Comparison of the experimental IR spectra with the predictions of density functional theory calculations (DFT, B3LYP D3BJ/6-31+G(d)) leads to assignments for the three conformers, all of which possess tightly folded alkyl chains that enable formation of a T-H (conformer A) or H-T (conformers B and C) hydrogen bonds. A modified version of the generalized Amber force field was developed to more accurately describe the hydroxamic acid OH internal rotor potential, leading to predictions for the relative energies in reasonable agreement with experiment. This force field was used to generate a disconnectivity graph for the low-energy portion of the potential energy landscape of SAHA. This disconnectivity graph contains more than one hundred minima and maps out the lowest-energy pathways between them, which could then be characterized via DFT calculations. This combination of force field and DFT calculations provides insight into the potential energy landscape and how population was funneled into the three observed conformers.

•Supersonic jet FT microwave spectra in the ground vibrational state.•Methyl butyrate exists under jet conditions in both Cs and C1 symmetry forms.•Molecular and internal dynamics parameter determined with very high accuracy.•2D potential energy surface for conformational preferences.•Collisional removal of population from the high energy conformers is observed.The broadband rotational spectrum of methyl butyrate from 8 to 18 GHz, recorded using a chirp-pulsed Fourier transform microwave (FTMW) spectrometer, was combined with high resolution FTMW measurements over the 2–26.5 GHz region to provide a comprehensive account of its microwave spectrum under jet-cooled conditions. Two low-energy conformers, one with a fully extended, heavy-atom planar anti/anti structure (a, a), and the other with a gauche propyl chain (g±, a), were assigned in the spectrum. Torsional A/E splittings due to the internal rotation of the methoxy methyl group were resolved for both lower energy conformers, and were fitted using the program XIAM and BELGI, providing an estimate of the barrier to methyl internal rotation of V3 ≈ 420 cm−1. The conformational landscape of methyl butyrate occurs on a two-dimensional potential energy surface, which was mapped out by quantum chemical calculations at the B2PLYP-D3BJ/aug-cc-pVTZ level of theory. The low torsional barrier about the CC(O)O bond leads to collisional removal of population originally in the (a, g±) and (g±, g±) minima into the (a, a) and (g±, a) minima, respectively, during the cooling in the expansion. Analysis of experimental intensities in the spectrum provide percent populations downstream in the expansion of 41 ± 4% (a, a), and 59 ± 6% (g±, a).Download high-res image (112KB)Download full-size image

The conformational preferences of pentyl- through decylbenzene are studied under jet-cooled conditions in the gas phase. Laser-induced fluorescence excitation spectra, fluorescence-dip infrared spectra in the alkyl CH stretch region, and Raman spectra are combined to provide assignments for the observed conformers. Density functional theory calculations at the B3LYP-D3BJ/def2TZVP level of theory provide relative energies and normal mode vibrations that serve as inputs for an anharmonic local mode theory introduced in earlier work on alkylbenzenes with n = 2–4. This model explicitly includes anharmonic mixing of the CH stretch modes with the overtones of scissors/bend modes of the CH2 and CH3 groups in the alkyl chain, and is used to assign and interpret the single-conformation IR spectra. In octylbenzene, a pair of LIF transitions shifted −92 and −78 cm−1 from the all-trans electronic origin have unique alkyl CH stretch transitions that are fit by the local model to a g1g3g4 conformation in which the alkyl chain folds back over the aromatic ring π cloud. Its calculated energy is only 1.0 kJ mol−1 above the all-trans global minimum. This fold is at an alkyl chain length less than half that of the pure alkanes (n = 18), consistent with a smaller energy cost for the g1 dihedral and the increased dispersive interaction of the chain with the π cloud. Local site frequencies for the entire set of conformers from the local mode model show ‘edge effects’ that raise the site frequencies of CH2(1) and CH2(2) due to the phenyl ring and CH2(n − 1) due to the methyl group. The g1g3g4 conformer also shows local sites shifted up in frequency at CH2(3) and CH2(6) due to interaction with the π cloud.

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′ β-turn around Gly3-Phe4 and a γ-turn around Gly2, providing spectroscopic evidence for the formation of a β-hairpin hydrogen bonding pattern. Rather than disrupting the peptide backbone structure, the protonated N-terminus serves to stabilize the β-hairpin by positioning itself in a pocket above the turn where it can form H-bonds to the Gly3 and C-terminus C═O groups. This β-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].

The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

The rotational spectra of the amino alcohols d-allo-threoninol, 2-amino-1,3-propanediol, and 1,3-diamino-2-propanol and the triamine analog, propane-1,2,3-triamine, have been investigated under jet-cooled conditions over the 7.5–18.5 GHz frequency range using chirped-pulsed Fourier transform microwave spectroscopy. Microwave transitions due to three conformers of d-allothreoninol, four conformers of 2-amino-1,3-propanediol, four conformers of 1,3-diamino-2-propanol, and four conformers of propane-1,2,3-triamine have been identified and assigned, aided by comparison of the fitted experimental rotational constants with the predictions for candidate structures based on an exhaustive conformational search using force field, ab initio and DFT methods. Distinctions between conformers with similar rotational constants were made on the basis of the observed nuclear quadrupole splittings and relative line strengths, which reflect the direction of the permanent dipole moment of the conformers. With three adjacent H-bonding substituents along the alkyl chain involving a combination of OH and NH2 groups, hydrogen-bonded cycles (3 H-bonds) and chains (2 H-bonds) remain close in energy, no matter what the OH/NH2 composition. Two families of H-bonded chains are possible, with H-bonding substituents forming curved chain or extended chain structures. Percent populations of the observed conformers were extracted from the relative intensities of their microwave spectra, which compare favorably with relative energies calculated at the B2PLYP-D3BJ/aug-cc-pVTZ level of theory. In glycerol (3 OH), d-allothreoninol (2 OH, 1 NH2), 2-amino-1,3-propanediol (2 OH, 1 NH2), and 1,3-diamino-2-propanol (1 OH, 2 NH2), H-bonded cycles are most highly populated, followed by curved chains (3 OH or 2 OH/1 NH2) or extended chains (1 OH/2 NH2). In propane-1,2,3-triamine (3 NH2), H-bonded cycles are pushed higher in energy than both curved and extended chains, which carry all the observed population. The NH2 group serves as a better H-bond acceptor than donor, as is evidenced by optimized structures in which H-bond lengths fall into the following order: r(OH···N) ≈ r(OH···O) < r(NH···N) ≈ r(NH···O).

The electronic and infrared spectra of the 5-methyl-2-furanylmethyl (MFM) radical have been characterized under jet-cooled conditions in the gas phase. This resonance-stabilized radical is formed by H atom loss from one of the methyl groups of 2,5-dimethylfuran (DMF), a promising second-generation biofuel. As a resonance-stabilized radical, it plays an important role in the flame chemistry of DMF. The D0–D1 transition was studied using two-color resonant two-photon ionization (2C-R2PI) spectroscopy. The electronic origin is in the middle of the visible spectrum (21934 cm–1 = 455.9 nm) and is accompanied by Franck–Condon activity involving the hindered methyl rotor. The frequencies and intensities are fit to a one-dimensional methyl rotor potential, using the calculated form of the ground state potential. The methyl rotor reports sensitively on the local electronic environment and how it changes with electronic excitation, shifting from a preferred ground state orientation with one CH in-plane and anti to the furan oxygen, to an orientation in the excited state in which one CH group is axial to the plane of the furan ring. Ground and excited state alkyl CH stretch infrared spectra are recorded using resonant ion-dip infrared (RIDIR) spectroscopy, offering a complementary view of the methyl group and its response to electronic excitation. Dramatic changes in the CH stretch transitions with electronic state reflect the changing preference for the methyl group orientation.

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 β-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 β-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 β-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.

•UV spectrum of cold (<10 K) protonated leucine enkephalin via action spectroscopy.•IR spectrum of cold protonated leucine enkephalin via IR–UV double resonance.•DFT calculated structures and vibrational frequency analyses of cold protonated leucine enkephalin.•Assigned conformational family of structures for cold protonated leucine enkephalin.We have applied ultraviolet and infrared–ultraviolet (IR–UV) double resonance photofragment spectroscopy in a tandem mass spectrometer for the spectroscopic characterization of cryogenically-cooled protonated leucine enkephalin (H+-YGGFL), for the purposes of elucidating its three-dimensional structure. The primary UV-induced photofragmentation pathway following excitation of the tyrosine chromophore is loss of the tyrosine side chain (107 Da). IR-enhanced photofragmentation via this channel makes IR–UV depletion spectroscopy difficult, and IR photofragment gain spectroscopy is used instead to record the infrared spectrum in the hydride stretch and amide I/II regions. By comparing the experimental spectrum with the predictions of DFT M05-2X/6-31+G(d) calculations, a single backbone structure was assigned that is similar to, but distinct from, that assigned in the recent work of Polfer et al. [15]. Additionally, the assigned structure’s theoretical cross-section is comparable to previous ion mobility results. The structure is characterized by a compact hydrogen-bonding architecture in which the peptide backbone self-solvates the N-terminal ammonium group carrying the charge. In addition to H-bonds to the tyrosine π cloud and the second glycine carbonyl oxygen, the ammonium group is involved in a series of cooperatively strengthened H-bonds between the N and C termini, linking the COOH group to the FL peptide bond. The resulting structure suggests some relevance to the fragmentation pathways of protonated YGGFL.

The ultraviolet spectroscopy of isoelectronic pair para-diisocyanobenzene (pDIB) and para-isocyanobenzonitrile (pIBN) has been studied under gas-phase, jet-cooled conditions. These molecules complete a sequence of mono and disubstituted nitrile/isonitrile benzene derivatives, enabling a comparison of the electronic effects of such substitution. Utilizing laser-induced fluorescence (LIF) and resonant two-photon ionization (R2PI) spectroscopy, the S0–S1 electronic origins of pDIB and pIBN have been identified at 35 566 and 35 443 cm–1, respectively. In pDIB, the S0–S1 origin is very weak, with b3g fundamentals induced by vibronic coupling to the S2 state dominating the spectrum at 501 cm–1 (ν17, isocyano bend) and 650 cm–1 (ν16, ring distortion). The spectrum extends over 5000 cm–1, remaining sharp and relatively uncongested over much of this range. Dispersed fluorescence (DFL) spectra confirm the dominating role played by vibronic coupling and identify Franck–Condon active ring modes built off the vibronically-induced bands. In pDIB, the S2 state has been tentatively observed at about 6100 cm–1 above the S0–S1 origin. In pIBN, the S0–S1 origin is considerably stronger, but vibronic coupling still plays an important role, involving fundamentals of b2 symmetry. The bending mode of the nitrile group dominates the vibronically-induced activity. Calculations carried out at the TD-DFT B3LYP/6-31+G(d) level of theory account for the extremely weak S0–S1 oscillator strength of pDIB and the larger intensity of the S0–S1 origins of pIBN and pDCB (para-dicyanobenzene) as nitrile groups are substituted for isonitrile groups. In pDIB, a nearly perfect cancellation of transition dipoles occurs due to two one-electron transitions that contribute nearly equally to the S0–S1 transition. The spectra of both molecules show no clear evidence of charge-transfer interactions that play such an important role in some cyanobenzene derivatives.

Ultraviolet photofragmentation spectroscopy and infrared spectroscopy were performed on two prototypical guaiacyl (G)-type dilignols containing β-O-4 and β–β linkages, complexed with either lithium or sodium cations. The complexes were generated by nanoelectrospray ionization, introduced into a multistage mass spectrometer, and subsequently cooled in a 22-pole cold ion trap to T ≈ 10 K. A combination of UV photofragment spectroscopy and IR-UV double resonance spectroscopy was used to characterize the preferred mode of binding of the alkali metal cations and the structural changes so induced. Based on a combination of spectral evidence provided by the UV and IR spectra, the Li+ and Na+ cations are deduced to preferably bind to both dilignols via their linkages, which constitute unique, oxygen-rich binding pockets for the cations. The UV spectra reflect this binding motif in their extensive Franck–Condon activity involving low-frequency puckering motions of the linkages in response to electronic excitation. In the pinoresinol•Li+/Na+ complexes involving the β–β linkage, the spectra also showed an inherent spectral broadening. The photofragment mass spectra are unique for each dilignol•Li+/Na+ complex, many of which are also complementary to those produced by collision-induced dissociation (CID), indicating the presence of unique excited state processes that direct the fragmentation. These results suggest the potential for site-selective fragmentation and for uncovering fragmentation pathways only accessed by resonant UV excitation of cold lignin ions.

The water hexamer and heptamer are the smallest sized water clusters that support three-dimensional hydrogen-bonded networks, with several competing structures that could be altered by interactions with a solute. Using infrared–ultraviolet double resonance spectroscopy, we record isomer-specific OH stretch infrared spectra of gas-phase benzene-(H2O)6,7 clusters that demonstrate benzene’s surprising role in reshaping (H2O)6,7. The single observed isomer of benzene-(H2O)6 incorporates an inverted book structure rather than the cage or prism. The main conformer of benzene-(H2O)7 is an inserted-cubic structure in which benzene replaces one water molecule in the S4-symmetry cube of the water octamer, inserting itself into the water cluster by engaging as a π H-bond acceptor with one water and via C—H···O donor interactions with two others. The corresponding D2d-symmetry inserted-cube structure is not observed, consistent with the calculated energetic preference for the S4 over the D2d inserted cube. A reduced-dimension model that incorporates stretch–bend Fermi resonance accounts for the spectra in detail and sheds light on the hydrogen-bonding networks themselves and on the perturbations imposed on them by benzene.

Ultraviolet spectroscopy of sinapoyl malate, an essential UV-B screening agent in plants, was carried out in the cold, isolated environment of a supersonic expansion to explore its intrinsic UV spectral properties in detail. Despite these conditions, sinapoyl malate displays anomalous spectral broadening extending well over 1000 cm–1 in the UV-B region, presenting the tantalizing prospect that nature’s selection of UV-B sunscreen is based in part on the inherent quantum mechanical features of its excited states. Jet-cooling provides an ideal setting in which to explore this topic, where complications from intermolecular interactions are eliminated. In order to better understand the structural causes of this behavior, the UV spectroscopy of a series of sinapate esters was undertaken and compared with ab initio calculations, starting with the simplest sinapate chromophore sinapic acid, and building up the ester side chain to sinapoyl malate. This “deconstruction” approach provided insight into the active mechanism intrinsic to sinapoyl malate, which is tentatively attributed to mixing of the bright V (1ππ*) state with an adiabatically lower 1nπ* state which, according to calculations, shows unique charge-transfer characteristics brought on by the electron-rich malate side chain. All members of the series absorb strongly in the UV-B region, but significant differences emerge in the appearance of the spectrum among the series, with derivatives most closely associated with sinapoyl malate showing characteristic broadening even under jet-cooled conditions. The long vibronic progressions, conformational distribution, and large oscillator strength of the V (ππ*) transition in sinapates makes them ideal candidates for their role as UV-B screening agents in plants.

Single-conformation ultraviolet and infrared spectroscopy was performed on dilignols containing two of the three biologically prevalent β-lignol linkages, erythro β–O–4 (β-aryl ether) and (±) β–β (pinoresinol). Both dilignols contain guaiacol(G)-type sub-units, representative of these linkages in G-type lignin. Resonant two-photon ionization (R2PI), IR-UV, and UV-UV holeburning (UVHB) spectroscopy in the cold, isolated environment of a supersonic expansion was carried out to determine the spectroscopic signatures associated with each linkage conformation, revealing striking differences in the vibronic intensity patterns between the two molecules in the UV. Two conformational isomers were found for the β–O–4 dilignol, both being classified into the fully hydrogen-bonded family with α-OH⋯OCH3 (C8) and γ-OH⋯Oβ (C5) H-bonds that are characteristic of the β–O–4 linkage. Conversely, a single dominant conformation was found for the conformationally-constrained pinoresinol. Resonant ion-dip infrared (RIDIR) spectroscopy provided conformation-specific IR spectra in the OH stretch and alkyl CH stretch regions, yielding complementary data that reported on both the intramolecular H-bonding and more subtle linkage features, respectively. DFT M05-2X calculations predict that the rigid β–β linkage had far fewer low-energy conformations in the first 20 kJ mol−1 (3) than the more flexible β–O–4 linkage (45). In the β–O–4 lignin dimer, the distinct UV chromophores lead to a splitting between S1 and S2 states that is determined mainly by the differences in the chemical structures of the two chromophores. In pinoresinol however, the assigned structure has C2 symmetry, with a calculated vertical excitonic splitting between the S1 and S2 states of 74 cm−1 (TDDFT). After taking into account the reduction in splitting associated with the geometry change in the aromatic rings upon electronic excitation, a vibronically quenched excitonic splitting of no more than a few wavenumbers is predicted for the C2 symmetric pinoresinol, but a definite experimental confirmation was not possible. These results predict that, under most circumstances, adjacent chromophores along a lignin polymer chain are not significantly electronically coupled to one another, and can be treated largely as isolated chromophores.

A theoretical model Hamiltonian [J. Chem. Phys. 2013, 138, 064308] for describing vibrational spectra associated with the CH stretch of CH2 groups is extended to molecules containing methyl and methoxy groups. Results are compared to the infrared (IR) spectroscopy of four molecules studied under supersonic expansion cooling in gas phase conditions. The molecules include 1,1-diphenylethane (DPE), 1,1-diphenylpropane (DPP), 2-methoxyphenol (guaiacol), and 1,3-dimethoxy-2-hydroxybenzene (syringol). Transforming the bending normal mode vibrations of CH3 groups to local scissor vibrations leads to model Hamiltonians which share many features present in our model Hamiltonian for the stretching vibrations of CH2 Fermi coupled to scissor modes. The central difference arises from the greater scissor–scissor coupling present in the CH3 case. Comparing anharmonic couplings between these modes and the stretch–bend Fermi coupling for a variety of systems, it is observed that the anharmonic couplings are robust; their values are similar for the four molecules studied as well as for ethane and methanol. Similar results are obtained with both density functional theory and coupled-cluster calculations. This robustness suggests a new parametrization of the model Hamiltonian that reduces the number of fitting parameters. In contrast, the harmonic contributions to the Hamiltonian vary substantially between the molecules leading to important changes in the spectra. The resulting Hamiltonian predicts most of the major spectral features considered in this study and provides insights into mode mixing and the consequences of the mixing on dynamical processes that follow ultrafast CH stretch excitation.

The folding preferences of two capped, constrained β/γ-dipeptide isomers, Ac-βACPC-γACHC-NHBn and Ac-γACHC-βACPC-NHBn, (designated βγ and γβ, respectively), have been investigated using single- and double-resonance ultraviolet and infrared spectroscopy in the gas phase. These capped β/γ-dipeptides have the same number of backbone atoms between their N- and C-termini as a capped α-tripeptide and thus serve as a minimal structural unit on which to test their ability to mimic the formation of the first turn of an α-helix. Resonant two-photon ionization and UV–UV hole-burning spectroscopy were performed in the S0–S1 region, revealing the presence of three unique conformations of βγ and a single conformation of γβ. Resonant ion-dip infrared spectra were obtained in the NH stretch region from 3300 to 3500 cm–1 and in both the amide I and amide II regions from 1400 to 1800 cm–1. These infrared spectra were compared to computational predictions from density functional theory calculations at the M05-2X/6-31+G(d) level, leading to assignments for the observed conformations. Two unique bifurcated C8/C13 H-bonded ring structures for βγ and a single bifurcated C9/C13 H-bonded ring structure for γβ were observed. In all cases, the H-bonding patterns faithfully mimic the first full turn of an α-helix, most notably by containing a 13-membered H-bonded cycle but also by orienting the interior amide group so that it is poised to engage in a second C13 H-bond as the β/γ-peptide lengthens in size. The structural characteristics of the β/γ-peptide version of the 13-helix turn are compared with the α-helix counterpart and with a reported crystal structure for a longer β/γ-peptide oligomer.

Chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) is combined with a flash pyrolysis (hyperthermal) microreactor as a novel method to investigate the molecular structure of cyclopentadienone (C5H4═O), a key reactive intermediate in biomass decomposition and aromatic oxidation. Samples of C5H4═O were generated cleanly from the pyrolysis of o-phenylene sulfite and cooled in a supersonic expansion. The 13C isotopic species were observed in natural abundance in both C5H4═O and in C5D4═O samples, allowing precise measurement of the heavy atom positions in C5H4═O. The eight isotopomers include: C5H4═O, C5D4═O, and the singly 13C isotopomers with 13C substitution at the C1, C2, and C3 positions. Microwave spectra were interpreted by CCSD(T) ab initio electronic structure calculations and an re molecular structure for C5H4═O was found. Comparisons of the structure of this “anti-aromatic” molecule are made with those of comparable organic molecules, and it is concluded that the disfavoring of the “anti-aromatic” zwitterionic resonance structure is consistent with a more pronounced C═C/C—C bond alternation.Keywords: antiaromatic; Chen nozzle; chirped-pulse Fourier transform microwave spectroscopy; cyclopentadienone; flash pyrolysis microreactor; hyperthermal nozzle; reactive intermediate;

[2.2.2]Paracylcophane (tricyclophane, TCP) is a macrocycle with three phenyl substituents linked by ethyl bridges (−CH2CH2−) in the para-position, forming an aromatic-rich pocket capable of binding various substituents, including nature’s solvent, water. Building on previous work [Buchanan, E. G.; et al. J. Chem. Phys. 2013, 138, 064308] that reported on the ground state conformational preferences of TCP, the focus of the present study is on the infrared and ultraviolet spectroscopy of TCP–(H2O)n clusters with n = 1–5. Resonant two-photon ionization (R2PI) was used to interrogate the mass selected electronic spectrum of the clusters, reporting on the perturbations imposed on the electronic states of TCP as the size of the water clusters bound to it vary in size from n = 1–5. The TCP–(H2O)n S0–S1 origins are shifted to lower frequency from the monomer, indicating an increased binding energy of the water or water network in the excited state. Ground state resonant ion-dip infrared (RIDIR) spectra of TCP–(H2O)n (n = 1–5) clusters were recorded in the OH stretch region, which probes the H-bonded water networks present and the perturbations imposed on them by TCP. The experimental frequencies are compared with harmonic vibrational frequencies calculated using density functional theory (DFT) with the dispersion-corrected functional ωB97X-D and a 6-311+g(d,p) basis set, providing firm assignments for their H-bonding structures. The H2O molecule in TCP–(H2O)1 sits on top of the binding pocket, donating both of its hydrogen atoms to the aromatic-rich interior of the monomer. The antisymmetric stretch fundamental of H2O in the complex is composed of a closely spaced set of transitions that likely reflect contributions from both para- and ortho-forms of H2O due to internal rotation of the H2O in the binding pocket. TCP–(H2O)2 also exists in a single conformational isomer that retains the same double-donor binding motif for the first water molecule, with the second H2O acting as a donor to the first, thereby forming a water dimer. The OH stretch infrared spectrum reflects a cooperative strengthening of both π-bound and OH···O H-bonds due to binding to TCP. The TCP–(H2O)n, n = 3–5 clusters all form H-bonded cycles, retaining their preferred structures in the absence of TCP, but distorted significantly by the presence of the TCP molecule. TCP–(H2O)3 divides its population between two conformational isomers that differ in the direction of the H-bonds in the cycle, either clockwise or counterclockwise, which are distinguishable by virtue of the C2 symmetry of the TCP monomer. TCP–(H2O)4 and TCP–(H2O)5 have OH stretch IR spectra that are close analogues of their benzene–(H2O)n counterparts in the H-bonded OH stretch region, but differ somewhat in the free and π OH stretch regions as the tetramer and pentamer cycles begin to spill out of the pocket interior. Lastly, excited state RIDIR spectroscopy in the OH stretch region is used to probe the response of water cluster to ultraviolet excitation, showing how the proximity of a given water molecule to the aromatic-rich π clouds affects the infrared spectrum of the water network.

The seven most stable conformers of d-threoninol (2(S)-amino-1,3(S)-butanediol), a template used for the synthesis of artificial nucleic acids, have been identified and characterized from their pure rotational transitions in the gas phase using chirped-pulse Fourier transform microwave spectroscopy. d-Threoninol is a close analogue of glycerol, differing by substitution of an NH2 group for OH on the C(β) carbon and by the presence of a terminal CH3 group that breaks the symmetry of the carbon framework. Of the seven observed structures, two are H-bonded cycles containing three H-bonds that differ in the direction of the H-bonds in the cycle. The other five are H-bonded chains containing OH···NH···OH H-bonds with different directions along the carbon framework and different dihedral angles along the chain. The two structural types (cycles and chains of H-bonds) are in surprisingly close energetic proximity. Comparison of the rotational constants with the calculated structures at the MP2/6-311++G(d,p) level of theory reveals systematic changes in the H-bond distances that reflect NH2 as a better H-bond acceptor and poorer donor, shrinking the H-bond distances by ∼0.2 Å in the former case and lengthening them by a corresponding amount in the latter. Thus revealed is the subtle effect of asymmetric substitution on the energy landscape of a simple molecule, likely to be important in living systems.

•A novel tandem MS based instrument for the spectroscopic interrogation of cold gas phase ions has been constructed.•A dual linear ion trap based triple quadrupole intersects a spectroscopic axis containing a 22-pole ion trap cooled to 10 K.•A novel tandem MS based instrument has been constructed.A novel tandem mass spectrometry based instrument for the spectroscopic interrogation of cold gas phase polyatomic ions has been constructed. The instrument consists of a dual linear ion trap (LIT) based triple quadrupole axis intersecting a spectroscopic axis containing a 22-pole ion trap cooled to 5 K. The triple quadrupole axis intersects the spectroscopy axis between the second and third quadrupoles, which are separated by an ion deflector that is used to direct ion injection into the cold ion trap from the second quadrupole and subsequently to direct ions ejected from the cold ion trap into the third quadrupole. Both the second and third quadrupoles can be operated as LITs capable of dipolar excitation across opposing quadrupole rods. Broad-band or single-frequency waveforms can be used to effect mass selection or mass analysis, respectively. The dual ion trapping capability allows for ion accumulation to occur in parallel with ion spectroscopy and mass analysis, thereby improving the overall efficiency of the experiment. Extensive use of homebuilt equipment has allowed for maximum flexibility, with capabilities for using ion/ion reactions in the ion generation step, and IR-UV double resonance spectroscopy during ion interrogation.

Single-conformation spectroscopy has been used to study two cyclically constrained and capped γ-peptides: Ac-γACHC-NHBn (hereafter γACHC, Figure 1a), and Ac-γACHC-γACHC-NHBn (γγACHC, Figure 1b), under jet-cooled conditions in the gas phase. The γ-peptide backbone in both molecules contains a cyclohexane ring incorporated across each Cβ-Cγ bond and an ethyl group at each Cα. This substitution pattern was designed to stabilize a (g+, g+) torsion angle sequence across the Cα–Cβ–Cγ segment of each γ-amino acid residue. Resonant two-photon ionization (R2PI), infrared–ultraviolet hole-burning (IR–UV HB), and resonant ion-dip infrared (RIDIR) spectroscopy have been used to probe the single-conformation spectroscopy of these molecules. In both γACHC and γγACHC, all population is funneled into a single conformation. With RIDIR spectra in the NH stretch (3200–3500 cm–1) and amide I/II regions (1400–1800 cm–1), in conjunction with theoretical predictions, assignments have been made for the conformations observed in the molecular beam. γACHC forms a single nearest-neighbor C9 hydrogen-bonded ring whereas γγACHC takes up a next-nearest-neighbor C14 hydrogen-bonded structure. The gas-phase C14 conformation represents the beginning of a 2.614-helix, suggesting that the constraints imposed on the γ-peptide backbone by the ACHC and ethyl groups already impose this preference in the gas-phase di-γ-peptide, in which only a single C14 H-bond is possible, constituting one full turn of the helix. A similar conformational preference was previously documented in crystal structures and NMR analysis of longer γ-peptide oligomers containing the γACHC subunit [Guo, L., et al. Angew. Chem. Int. Ed. 2011, 50, 5843−5846]. In the gas phase, the γACHC-H2O complex was also observed and spectroscopically interrogated in the molecular beam. Here, the monosolvated γACHC retains the C9 hydrogen bond observed in the bare molecule, with the water acting as a bridge between the C-terminal carbonyl and the π-cloud of the UV chromophore. This is in contrast to the unconstrained γ-peptide-H2O complex, which incorporates H2O into both C9 and amide-stacked conformations.

1,2-Diphenoxyethane (C6H5–O–CH2–CH2–O–C6H5, DPOE) is a flexible bichromophore in which the two phenyl rings are separated from one another by an −O–CH2–CH2–O– chain with five flexible dihedral angles about which hindered rotation can occur. As such, it is a phenyl capped analog of dimethoxyethane (DMOE), which has served as a model compound for development of force fields for polyethylene glycol (PEG). The ground state conformational energy landscape of DPOE is explored using a combination of single-conformation spectroscopy of the jet-cooled molecule and calculations of the conformational minima and transition states. In the experimental UV spectrum, ultraviolet hole-burning establishes the presence of just two conformations with significant population in the supersonic jet expansion. Fluorescence dip infrared (FDIR) spectroscopy is used to record infrared spectra of the two conformers in the alkyl CH stretch, CH bend, and CO stretch regions. When compared with harmonic vibrational frequency calculations, the two isomers are determined to be of C2h and C2 symmetry, and labeled ttt and tgt to denote the three central dihedrals as trans or gauche. Infrared population transfer spectroscopy is used to determine fractional abundances for the two conformers (fttt= 0.53 ± 0.01; ftgt =0.47 ± 0.01). Relaxed potential energy curves along the three nonequivalent dihedral angles are used to map out the shape of the potential energy landscape that leads to these preferences. The Fermi resonance in the alkyl CH stretch spectrum is successfully modeled using a recently developed methodology [Buchanan et al., J. Chem. Phys.2013, 138, 064308] employing a reduced dimension Hamiltonian. The scissor overtones couple to the CH2 symmetric stretch and only indirectly to the asymmetric stretch through symmetric stretch/asymmetric stretch coupling. The presence of the oxygen atoms in the chain shifts the CH scissor overtones to higher frequencies than in pure alkyl chains, qualitatively changing the spectral consequences of the Fermi resonance, with the scissor overtones now appearing as the highest frequency bands in the spectrum. The spectra are contrasted with those in 1,2-diphenylethane, a close analog with a very different appearance to its CH stretch spectrum, in which the scissor overtones appear as the lowest frequency bands.

The capped α/γ-peptide foldamers Ac-γACHC-Ala-NH-benzyl (γα) and Ac-Ala-γACHC-NH-benzyl (αγ) were studied in the gas phase under jet-cooled conditions using single-conformation spectroscopy. These molecules serve as models for local segments of larger heterogeneous 1:1 α/γ-peptides that have recently been synthesized and shown to form a 12-helix composed of repeating C12 H-bonded rings both in crystalline form and in solution [Guo, L.; et al. J. Am. Chem. Soc. 2009, 131, 16018]. The γα and αγ peptide subunits are structurally constrained at the Cβ–Cγ bond of the γ-residue with a cis-cyclohexyl ring and by an ethyl group at the Cα position. These triamides are the minimum length necessary for the formation of the C12 H-bond. Resonant two-photon ionization (R2PI) provides ultraviolet spectra that have contributions from all conformational isomers, while IR-UV hole-burning (IR-UV HB) and resonant ion-dip infrared (RIDIR) spectroscopies are used to record single-conformation UV and IR spectra, respectively. Four and six conformers are identified in the R2PI spectra of the γα and αγ peptides, respectively. RIDIR spectra in the NH stretch, amide I (C═O stretch), and amide II (NH bend) regions are compared with the predictions of density functional theory (DFT) calculations at the M05-2X/6-31+G* level, leading to definite assignments for the H-bonding architectures of the conformers. While the C12 H-bond is present in both γα and αγ, C9 rings are more prevalent, with seven of ten conformers incorporating a C9 H-bond involving in the γ-residue. Nevertheless, comparison of the assigned structures of gas-phase γα and αγ with the crystal structures for γα and larger α/γ-peptides reveals that the constrained γ-peptide backbone formed by the C9 ring is structurally similar to that formed by the larger C12 ring present in the 12-helix. These results confirm that the ACHC/ethyl constrained γ-residue is structurally preorganized to play a significant role in promoting C12 H-bond formation in larger α/γ-peptides.

The state-dependent spectroscopy of α-methylbenzyl radical (α-MeBz) has been studied under jet-cooled conditions. Two-color resonant two-photon ionization (2C-R2PI), laser-induced fluorescence, and dispersed fluorescence spectra were obtained for the D0–D1 electronic transition of this prototypical resonance-stabilized radical in which the methyl group is immediately adjacent to the primary radical site. Extensive Franck–Condon activity in hindered rotor levels was observed in the excitation spectrum, reflecting a reorientation of the methyl group upon electronic excitation. Dispersed fluorescence spectra from the set of internal rotor levels are combined with the excitation spectrum to obtain a global fit of the barrier heights and angular change of the methyl group in both D0 and D1 states. The best-fit methyl rotor potential in the ground electronic state (D0) is a flat-topped 3-fold potential (V3″ = 151 cm–1, V6″ = 34 cm–1) while the D1 state has a lower barrier (V3′ = 72 cm–1, V6′ = 15 cm–1) with Δφ = ± π/3, π, consistent with a reorientation of the methyl group upon electronic excitation. The ground state results are compared with calculations carried out at the DFT B3LYP level of theory using the 6-311+G(d,p) basis set, and a variety of excited state calculations are carried out to compare against experiment. The preferred geometry of the methyl rotor in the ground state is anti, which switches to syn in the D1 state and in the cation. The calculations uncover a subtle combination of effects that contribute to the shift in orientation and change in barrier in the excited state relative to ground state. Steric interaction favors the anti conformation, while hyperconjugation is greater in the syn orientation. The presence of a second excited state close by D1 is postulated to influence the methyl rotor properties. A resonant ion-dip infrared (RIDIR) spectrum in the alkyl and aromatic CH stretch regions was also recorded, probing in a complementary way the state-dependent conformation of α-MeBz. Using a scheme in which infrared depletion occurs between excitation and ionization steps of the 2C-R2PI process, analogous infrared spectra in D1 were also obtained, probing the response of the CH stretch fundamentals to electronic excitation. A reduced-dimension Wilson G-matrix model was implemented to simulate and interpret the observed infrared results. Finally, photoionization efficiency scans were carried out to determine the adiabatic ionization threshold of α-MeBz (IP = 6.835 ± 0.002 eV) and provide thresholds for ionization out of specific internal rotor levels, which report on the methyl rotor barrier in the cation state.

Size and conformation-specific ultraviolet and infrared spectra are used to probe the effects of binding a single water molecule on the close-lying excited states present in a model flexible bichromophore, 1,2-diphenoxyethane (DPOE). The water molecule binds to DPOE asymmetrically, thereby localizing the two electronically excited states on one or the other ring, producing a S1/S2 splitting of 190 cm–1. Electronic localization is reflected clearly in the OH stretch transitions in the excited states. Since the S2 origin is imbedded in vibronic levels of the S1 manifold, its OH stretch spectrum reflects the vibronic coupling between these levels, producing four OH stretch transitions that are a sum of contributions from S2-localized and S1-localized excited states. The single solvent water molecule thus plays multiple roles, localizing the electronic excitation in the bichromophore, inducing electronic energy transfer between the two rings, and reporting on the state mixing via its OH stretch absorptions.Keywords: excitonic splitting; gas-phase; internal mixing; jet-cooled; local modes; solvatochromic shift; surface hopping; vibronic coupling;

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.

Laser induced fluorescence (LIF) excitation scans and dispersed fluorescence (DFL) spectra have been recorded for two four-carbon α,ω-diphenyl systems, diphenyldiacetylene (DPDA, ϕ-CC–CC-ϕ) and trans-diphenylvinylacetylene (DPVA, ϕ-CHCH–CC-ϕ) as isolated molecules cooled in a supersonic expansion. While these molecules have similar conjugation length, they exhibit strikingly different vibronic spectroscopy and photophysics. The near-UV LIF excitation spectrum of diphenyldiacetylene has its electronic origin at 32158 cm−1, and a strong progression in the CC stretch (2156 cm−1). All transitions are inherently broad, with widths of ∼30 cm−1 fwhm or greater. The S1 origin DFL spectrum is composed of sharp transitions with Franck–Condon activity mirroring that in the excitation spectrum, and broad emission shifted well to the red ascribable to phosphorescence on the μs timescale. Using ab initio calculations, it is possible to show that DPDA exists as a single, planar conformer with D2h symmetry. In contrast, trans-diphenylvinylacetylene shows intense sharp transitions in both LIF and DFL spectra with an S0–S1 origin of 31183.2 cm−1 and long progressions involving the in-plane fundamentals ν53 (bridge-phenyl bending) and ν51 (bridge-phenyl stretch). A sharp reduction in fluorescence yield in DPVA occurs within 300 cm−1 of the S1 origin. Possible causes for the photophysical processes occurring in the two molecules are discussed.

Single-conformation spectroscopy of the three lignin monomers (hereafter “monolignols”) p-coumaryl alcohol (pCoumA), coniferyl alcohol (ConA), and sinapyl alcohol (SinA) has been carried out on the isolated molecules cooled in a supersonic expansion. Laser-induced fluorescence excitation, dispersed fluorescence, resonant two-photon ionization, UV−UV hole-burning, and resonant ion-dip infrared spectroscopy were carried out as needed to obtain firm assignments for the observed conformers of the three molecules. In each case, two conformers were observed, differing in the relative orientations of the vinyl and OH substituents para to one another on the phenyl ring. In pCoumA, the two conformers have S0−S1 origins nearly identical in size, split from one another by only 7 cm−1, in close analogy with previous results of Morgan et al. on p-vinylphenol ( Chem. Phys. 2008, 347, 340). ConA, with its methoxy group ortho to the OH group, also has two low-energy conformers forming a syn/anti pair, in this case with the OH group locked into an orientation in which it forms an intramolecular H-bond with the adjacent methoxy group. The electronic frequency shift between the two conformers is dramatically increased to 805 cm−1, with the dominant conformer of ConA (with S0−S1 origin at 32 640 cm−1) about 5 times the intensity of its minor counterpart (with S0−S1 origin at 33 444 cm−1). The presence of an OH···OCH3 intramolecular H-bond is established by the shift of the OH stretch fundamental of the OH group to 3599 cm−1, as it is in o-methoxyphenol (Fujimakiet al. J. Chem. Phys. 1999, 110, 4238). Analogous single-conformation UV and IR spectra of o-methoxy-p-vinylphenol show a close similarity to ConA and provide a basis for a firm assignment of the red-shifted (blue-shifted) conformer of both molecules to the syn (anti) conformer. The two observed conformers of SinA, with its two methoxy group straddling the OH group, have S0−S1 origins split by 239 cm−1 (33 055 and 33 294 cm−1), a value between those in pCoumA and ConA. A combination of experimental data and calculations on the three monolignols and simpler derivatives is used to establish that the conformational preferences of the monolignols reflect the preferences of each of the ring substituents separately, enhanced by the presence of the intramolecular OH···OCH3 H-bond. Taken as a whole, the presence of multiple flexible substituents locks in certain preferred orientations of the groups relative to one another, even in the apparently flexible allyl alcohol side chain (−CH═CH−CH2OH), where the OH group orients itself so that the hydrogen is pointed back over the vinyl π cloud in order to minimize interactions between the oxygen lone pairs and the π electrons.

Conformer-specific, vibrationally resolved electronic spectroscopy of benzylallene (4-phenyl-1,2-butadiene) is presented along with a detailed analysis of the products formed via its ultraviolet photoexcitation. Benzylallene is the minor product of the recombination of benzyl and propargyl radicals. The mass-selective resonant two-photon ionization spectrum of benzylallene was recorded under jet-cooled conditions, with its S0–S1 origin at 37 483 cm–1. UV–UV holeburning spectroscopy was used to show that only one conformer was present in the expansion. Rotational band contour analysis provided rotational constants and transition dipole moment direction consistent with a conformation in which the allene side chain is in the anti position, pointing away from the phenyl ring. The photochemistry of benzylallene was studied in a pump–probe geometry in which photoexcitation occurred by counter-propagating the expansion with a photoexcitation laser. The laser was timed to interact with the gas pulse in a short tube that extended the collisional region of the expansion. The products were cooled during expansion of the gas mixture into vacuum, before being interrogated using mass-selective resonant two-photon ionization. The UV–vis spectra of the photochemical products were compared to literature spectra for identification. Several wavelengths were chosen for photoexcitation, ranging from the S0–S1 origin transition (266.79 nm) to 193 nm. Comparison of the product spectral intensities as a function of photoexcitation wavelength provides information on the wavelength dependence of the product yields. Photoexcitation at 266.79 nm yielded five products (benzyl radical, benzylallenyl radical, 1-phenyl-1,3-butadiene, 1,2-dihydronaphthalene, and naphthalene), with naphthalene and benzylallenyl radicals dominant. At 193 nm, the benzylallenyl radical signal was greatly reduced in intensity, while three additional C10H8 isomeric products were observed. An extensive set of calculations of key stationary points on the ground state C10H10 and C10H9 potential energy surfaces were carried out at the DFT B3LYP/6-311G(d,p) level of theory. Mechanisms for formation of the observed products are proposed based on these potential energy surfaces, constrained by the results of cursory studies of the photochemistry of 1-phenyl-1,3-butadiene and 4-phenyl-1-butyne. A role for tunneling on the excited state surface in the formation of naphthalene is suggested by studies of partially deuterated benzylallene, which blocked naphthalene formation.

Mass-selective two-color resonant two-photon ionization (2C-R2PI) spectra of two resonance stabilized radicals (RSRs), 1-phenylallyl and benzylallenyl radicals, have been recorded under jet-cooled conditions. These two radicals, while sharing the same radical conjugation, have unique properties. The D0–D1 origin of the 1-phenylallyl radical is at 19208 cm−1, with extensive vibronic structure extending over 2000 cm−1 above the D1 origin. Much of this structure is assigned based on comparison with DFT and TDDFT calculations. Two-color photoionization efficiency scans reveal a sharp ionization threshold, providing a precise adiabatic ionization potential for the radical of 6.905(2) eV. By comparison, the benzylallenyl radical has an electronic origin at 19703 cm−1 and Franck–Condon activity similar to phenylallyl. The photoionization efficiency curve shows a gradual onset with apparent threshold at ∼7.50(2) eV. Visible–visible holeburning was used to show that each radical exists in one isomeric form in the expansion. The CH stretch IR spectrum of each radical was taken using D0-resonant ion dip infrared spectroscopy (D0-RIDIRS) in a novel four-laser experiment. Comparison of the IR spectrum with the predictions of DFT B3LYP calculations leads to firm assignment of each radical as the trans isomer. TDDFT calculations on the excited states of benzylallenyl suggest the possibility that the excited state levels originally excited convert to an all-planar form prior to ionization. The potential role that these radicals could play in Titan's atmosphere as intermediates in formation pathways for polycyclic aromatic hydrocarbons (PAHs) is briefly discussed.

Rotationally resolved microwave and ultraviolet spectra of jet-cooled bis-(4-hydroxyphenyl)methane (b4HPM) have been obtained using Fourier-transform microwave and UV laser/molecular beam spectrometers. A recent vibronic level study of b4HPM [Rodrigo, C. P.; Müller, C. W.; Pillsbury, N. R.; James, W. H., III; Plusquellic, D. F.; Zwier, T. S. J. Chem. Phys.2011, 134, 164312] has assigned two conformers distinguished by the orientation of the in-plane OH groups and has identified two excitonic origins in each conformer. In the present study, the rotationally resolved bands of all four states have been well-fit to asymmetric rotor Hamiltonians. For the lower exciton (S1) levels, the transition dipole moment (TDM) orientations are perpendicular to the C2 symmetry axes and consist of 41(2):59(2) and 34(2):66(2)% a:c hybrid-type character. The S1 levels are therefore delocalized states of B symmetry and represent the antisymmetric combinations of the zero-order locally excited states of the p-cresol-like chromophores. The TDM polarizations of bands located at ≈132 cm–1 above the S1 origins are exclusively b-type and identify them as the upper exciton S2 origin levels of A symmetry. The TDM orientations and the relative band strengths from the vibronic study have been analyzed within a dipole–dipole coupling model in terms of the localized TDM orientations, μloc, on the two chromophores. The out-of-the-ring plane angles of μloc are both near 20° and are similar to results for diphenylmethane [Stearns, J. A.; Pillsbury, N. R.; Douglass, K. O.; Müller, C. W.; Zwier, T. S.; Plusquellic, D. F. J. Chem. Phys.2008, 129, 224305]. The in-plane angles are, however, rotated by 14 and 18° relative to DPM and, in part, explain the smaller than expected exciton splittings of these two conformers.

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-γ2-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-γ2-hPhe-N(Me)2 contains an additional methyl group relative to the previously studied Ac-γ2-hPhe-NHMe and therefore lacks the amide NH group responsible for C9 ring formation. Three conformations of Ac-γ2-hPhe-N(Me)2 are observed, all of which are amide-stacked structures. In a second new molecule, Ac-γ2-hPhe-NH(iPr), the C-terminal NHMe group of Ac-γ2-hPhe-NHMe is replaced with an NH(iPr) group. Three conformations of Ac-γ2-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-γ2-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.

The fluorescence spectroscopy of Z-phenylvinylacetylene (Z-PVA) has been studied under jet-cooled conditions. The laser-induced fluorescence (LIF) spectrum shows vibronic activity up to 600 cm−1 above the ππ* electronic origin at 33 838 cm−1. In contrast, the single vibronic level fluorescence spectrum of the electronic origin shows strong intensity in transitions ending in ground state levels at least 1200 cm−1 above the ground state zero-point level. The double-resonance technique of ultraviolet depletion (UVD) spectroscopy was used to show that there are strong absorptions in Z-PVA that are not observed in the LIF spectrum due to the turn of a nonradiative process in this electronic state. The LIF and UVD spectra were compared quantitatively to calculate the relative single vibronic level fluorescence quantum yields. Upon inspection, there are some indications of state specific effects; however, the nature of these effects is unclear. Ab initio and density functional theory calculations of the ground and excited states were used to map the first two excited states of Z-PVA along the C≡CH bending coordinate, determining them to be ππ* and πσ*, respectively, in character. The crossing of these two states is postulated to be the underlying reason for the observed loss in fluorescence intensity 600 cm−1 above the ππ* origin. The spectroscopy of Z-PVA has been compared to the previously characterized E isomer of phenylvinylacetylene [Liu, C. P., Newby, J. J., Muller, C. W., Lee, H. D., and Zwier, T. S. J. Phys. Chem. A 2008, 112 (39), 9454.].

Vibronic spectra of doublet−doublet transitions of 1-hydronaphthyl (1ΗΝ), 2-hydronaphthyl (2ΗΝ), and 1,2,3-trihydronaphthyl (THN, tetralyl) radicals have been recorded under jet-cooled conditions. Transitions due to the two C10H9 isomers were identified and assigned based on the choice of radical precursor, visible−visible hole-burning spectroscopy, comparison of observed vibronic transitions with calculation, and photoionization efficiency scans. The latter provided accurate ionization potentials for the three free radicals (IP(1ΗΝ) = 6.570 eV, IP(2ΗΝ) = 6.487 eV, IP(THN) = 6.620 eV, errors ±0.002 eV). A thermochemical cycle is used to extract from these ionization potentials the C−H bond dissociation energy (BDE) of 1HN at the 1-position of 121.2 ± 2 kJ/mol. Using proton affinities of 2ΗΝ and THN calculated at the G3(MP2, CC)//B3LYP/6-311G** level of theory, the corresponding C−H BDEs of 2HN at the 2-carbon (103.6 ± 2 kJ/mol) and of THN at the 3-position (168 ± 3 kJ/mol) are derived. The possible role played by these hydronaphthyl radicals in Titan’s atmosphere, the interstellar medium, and combustion are briefly discussed.

Attractive interactions between two carboxamide groups in a “stacked” geometry are explored under isolated molecule conditions. Infrared spectra of single conformations of a small γ-peptide, Ac-γ2-hPhe-NHMe, reveal the presence of a conformation in which the two amide planes are approximately parallel with the amide dipoles in an antialigned orientation. This stacked conformation is energetically comparable to conformations that contain an intramolecular amide−amide H-bond. Amide stacking interactions can compete with H-bonding in circumstances where the amide groups can be brought into a stacking configuration with minimal strain, opening the way for its use in the design of future foldamer structures.

Resonant two-photon ionization (R2PI), UV hole-burning (UVHB), and resonant ion-dip infrared (RIDIR) spectroscopies have been used to record single-conformation infrared and ultraviolet spectra of three model synthetic foldamers with heterogeneous backbones, α/β-peptides Ac-β3-hAla-l-Phe-NHMe (βαL), Ac-β3-hAla-d-Phe-NHMe (βαD), and Ac-l-Phe-β3-hAla-NHMe (αβL), isolated and cooled in a supersonic expansion. βαL and βαD are diastereomers, differing only in the configuration of the α-amino acid residue; βαL and αβL contain the same residues, but differ in residue order. In all three α/β-peptides the β3-residue has S absolute configuration. UVHB spectroscopy is used to determine that there are six conformers of each molecule and to locate and characterize their S0−S1 transitions in the origin region. RIDIR spectra in the amide NH stretch region reflect the number and strength of intramolecular H-bonds present. Comparison of the RIDIR spectra with scaled, harmonic vibrational frequencies and infrared intensities leads to definite assignments for the conformational families involved. C8/C7eq double-ring structures are responsible for three conformers of βαL and four of βαD, including those with the most intense transitions in the R2PI spectra. This preference for C8/C7eq double rings appears to be dictated by the C7eq ring of the α-peptide subunit. Three of the conformers of βαL and βαD form diastereomeric pairs (A/A′, C/C′, and G/G′) that have nearly identical S0−S1 origin positions in the UV and belong to the same conformational family, indicating no significant change associated with the change in chirality of the α-peptide subunit. However, βαL favors formation of a C6/C5 conformer over C11, while the reverse preference holds in βαD. Calculations indicate that the selective stabilization of the lowest-energy C11(g+) structure in βαD occurs because this structure minimizes steric effects between the β2 methylene group and C=O(1). In the α/β-peptide αβL, two conformers dominate the spectrum, one assigned to a C5/C8 bifurcated double-ring, and the other to a C5/C6 double-ring structure. This preference for C5 rings in the α/β-peptide occurs because the C5 ring is further stabilized by an amide NH···π interaction involving an NH group on the adjacent amide, as it is in the α-peptides. Comparison of the NH stretch spectra of C8/C7eq structures in βαL with their C7eq/C8 counterparts in αβL shows that the central amide NH stretch is shifted to lower frequency by some 50−70 cm−1 due to cooperative effects associated with the central amide accepting and donating a H-bond to neighboring amide groups. This swaps the ordering of the C8 and C7 NH stretch fundamentals in the two molecules.

The vibronic excitation spectrum of phenylcyclopenta-1,3-diene (PCP3D) has been recorded in a supersonic expansion using resonant-two-photon ionization (R2PI) and laser-induced fluorescence (LIF) techniques. The spectrum is dominated by the S0–S1 origin transition (31739 cm−1), with several low-frequency vibronic bands in the first 400 cm−1, followed by a sharp cut-off in intensity due to turn-on of a non-radiative process. Single vibronic level fluorescence (SVLF) spectra were recorded for the S1 origin and several vibronic bands of PCP3D. The excitation and emission spectra show that the molecule is planar with Cs symmetry in both the ground and excited states. Torsional potentials were simulated from the observed torsional structure in the excitation and emission spectra. The S0 potential (V2 = 1237 cm−1, V4 = −256 cm−1) is associated with a flat-bottomed potential supporting large inter-ring angular changes with little cost in energy (±36° at 200 cm−1), with a barrier of 1237 cm−1 at the perpendicular geometry. The S1 potential is much stiffer about the planar geometry, with a calculated barrier five times larger than in S0 (V2 = 6732 cm−1, V4 = −477 cm−1). Based on the torsional assignments, weak bands in the same frequency region assigned earlier to the structural isomer phenylcyclopenta-1,4-diene [J. J. Newby, J. A. Stearns, C. P. Liu and T. S. Zwier, J. Phys. Chem. A, 2007, 111, 10914–10927] have been re-assigned as hot bands arising from v″ = 1 in the inter-ring torsion, ν57.

The ultraviolet spectroscopy of the S1← S0 transition of 1-phenylcyclopentene (PCP) was studied by resonant-two-photon ionization (R2PI), laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF). UV–UV hole-burning (UVHB) spectroscopy was used to determine that there is only one spectroscopically distinct conformer in the supersonic expansion. The excitation spectrum shows extensive vibronic structure extending to over 1000 cm−1 above the electronic origin (34646 cm−1). Much of the vibronic structure is similar to that of styrene and other singly substituted benzene derivatives, with Franck–Condon (FC) activity predominantly in substituent-sensitive benzene modes. Sizeable FC progressions were also found in the inter-ring torsion, reflecting a large displacement in the inter-ring angle upon electronic excitation. No evidence for FC activity in the ring-puckering coordinate is observed. The torsional potentials of the ground and excited states were determined from the experimental transition frequencies by fitting the calculated to the experimental torsional frequency spacings in an automated least-squares fitting procedure. The S1 torsional potential is a symmetric single-well potential centered around a locally planar equilibrium geometry at a torsional angle of ϕ = 0°. The energy levels are reproduced by a cosine term potential function with torsional parameters V2 = 3765 cm−1 and V4 = −183 cm−1. The S0 torsional potential possesses a twisted equilibrium geometry that is strongly asymmetric about ϕ = 0° due to the non-planarity of the cyclopentene ring. The best-fit potential parameters uses a sin/cos potential function (odd/even), with Ve2 = 948 cm−1, Ve4 = −195 cm−1, Vo2 = −162 cm−1 and Vo4 = −268 cm−1. The shape of the potentials are similar to those predicted by relaxed potential energy scans calculated at the DFT, CIS and TDDFT//CIS levels of theory. The change in the torsional angle ϕ upon electronic excitation was determined to be ∼15° from fits of the displacement δ of the S0 torsional potential with respect to the S1 potential. The simulated shift of the S0 potential with respect to the S1 potential of ∼15° is in very good agreement with that obtained from B3LYP calculations.

Stimulated emission pumping-population transfer (SEP-PT) spectroscopy is used to experimentally determine upper and lower bounds on the energy thresholds to conformational isomerization between 14 X→Y reactant−product conformer pairs of isolated 5-phenyl-1-pentene (5PPene). This work builds directly on the spectroscopic assignments of the five observed conformers of 5PPene in the preceding paper. The observed thresholds fall into two energy ranges: near 600 cm−1 for isomerization processes that involve only reorientation of the terminal vinyl group, and in the 1200−1374 cm−1 range for barriers that involve hindered rotation about the alkyl chain carbon−carbon bonds. As a result, this latter threshold opens up much of the conformational phase space to exploration, with multiple isomerization pathways connecting any two of the conformational minima.

Laser-induced fluorescence, single-vibronic level fluorescence (SVLF), UV hole burning, and fluorescence dip infrared (FDIR) spectroscopy have been carried out on bis-(2-hydroxyphenyl)methane in order to characterize the ground-state and first excited-state vibronic spectroscopy of this model flexible bichromophore. These studies identified the presence of two conformational isomers. The FDIR spectra in the OH-stretch region determine that conformer A is an OH···O H-bonded conformer, while conformer B is a doubly OH···π H-bonded conformer with C2 symmetry. High-resolution ultraviolet spectra (∼50 MHz resolution) of a series of vibronic bands of both conformers confirm and refine these assignments. The transition dipole moment (TDM) direction in conformer A is consistent with electronic excitation that is primarily localized on the donor phenol ring. A tentative assignment of the S2 origin is made to a set of transitions ∼400 cm−1 above S1. In conformer B, the TDM direction firmly establishes C2 symmetry for the conformer in its S1 state and establishes the electronic excitation as delocalized over the two rings, as the lower member of an excitonic pair. The S2 state has not been clearly identified in the spectrum. Based on CIS calculations, the S2 state is postulated to be several times weaker than S1, making it difficult to identify, especially in the midst of overlap from vibronic bands due to conformer A. SVLF spectra show highly unusual vibronic intensity patterns, particularly in conformer B, which cannot be understood by simple harmonic Franck−Condon models, even in the presence of Duschinsky mixing. We postulate that these model flexible bichromophores have TDMs that are extraordinarily sensitive to the distance and orientation of the two aromatic rings, highlighting the need to map out the TDM surface and its dependence on the (up to) five torsional and bending coordinates in order to understand the observations.

The vibronic spectrum of tryptamine has been studied in a molecular beam up to an energy of 930 cm−1 above the S0−S1 electronic origin. Rotationally resolved electronic spectra reveal a rotation of the transition dipole moment direction from 1Lb to 1La beginning about 400 cm−1 above the 1Lb origin. In this region, vibronic bands which appear as single bands at low resolution contain rotational structure from more than one vibronic transition. The number of these transitions closely tracks the total vibrational state density in the 1Lb electronic state as a function of internal energy. Dispersed fluorescence spectra show distinct spectroscopic signatures attributable to the 1Lb and 1La character of the mixed excited-state wave functions. The data set is used to extrapolate to a 1La origin about 400 cm−1 above the 1Lb origin. DFT-MRCI calculations locate a conical intersection between these two states at about 900 cm−1 above the La origin, whose structure is located along a tuning coordinate which is close to a linear interpolation between the two excited-state geometries. Along the branching coordinate, there is no barrier from 1La to 1Lb. A two-tier model for the vibronic coupling is proposed.

Laser-induced fluorescence (LIF), resonant two-photon ionization (R2PI), ultraviolet hole-burning (UVHB), resonant ion-dip infrared (RIDIR), and infrared-infrared ultraviolet hole-burning (IR−IR−UV) spectroscopies were carried out on benzo-15-crown-5 ether−(H2O)n (B15C−(H2O)n) and 4′-amino-benzo-15-crown-5 ether−(H2O)n (ABC−(H2O)n) clusters with n = 1,2 formed in a supersonic expansion. Two isomers of B15C−(H2O)1 with S0−S1 origins at 35 628 and 35 685 cm−1 (B15C−(H2O)1(A) and B15C−(H2O)1(B), respectively) were identified and, on the basis of the combined evidence from the single-isomer UV and IR spectra, assigned to structures in which the H2O molecule donates both its OH groups to H-bonds to the crown oxygens. Both isomers share the same open, chairlike Cs symmetry structure for the crown ether that exposes the crown oxygen lone pairs to binding to H2O on the interior of the crown. This crown conformation is not among those represented in the observed conformers in the absence of the H2O molecule, indicating that even a single water molecule is capable of reshaping the crown binding pocket in binding to it. In B15C−(H2O)1(A), the water molecule takes up a position parallel to the crown plane of symmetry, using one OH group to bind to the two benzo oxygens, while the other OH binds to a single crown oxygen on the opposite side of the crown. The H2O molecule in B15C−(H2O)1(B) binds to the other two crown oxygens, in an orientation perpendicular to the crown’s symmetry plane. B15C−(H2O)2 also has two isomers. The first, B15C−(H2O)2(A) with S0−S1 origin at 35 813 cm−1, is assigned to a structure in which the two water molecules take up the two positions occupied by individual water molecules in B15C−(H2O)1 A and B. The second isomer, with S0−S1 origin at 35 665 cm−1, has an OH stretch RIDIR spectrum that reflects a water−water H-bond, with the second water molecule binding to the crown-bound water in the parallel binding site. The combined data from B15C−(H2O)1, ABC−(H2O)1, and ABC−(HOD) complexes is used to deduce the uncoupled OH stretch wavenumber shifts associated with each of the unique binding sites for H2O to the crown. Arguments are presented that the binding pocket present in benzo-15-crown-5 ether is of a near ideal size to accommodate strong bidentate binding of individual water molecules to its most open crown conformation.

Single-conformation spectroscopy of 5-phenyl-1-pentene has been studied in a supersonic expansion by using a combination of methods, including resonant two-photon ionization (R2PI), ultraviolet hole-burning (UVHB), and rotational band contour analysis. Five conformational isomers (labeled A−E) have been identified in the spectrum, with S0−S1 origins at 37518, 37512, 37526, 37577, and 37580 cm−1, respectively. Rotational band contours of these origin transitions recorded at 0.08 cm−1 resolution reflect the sensitivity of the direction of the transition dipole moment (TDM) to the conformation of the pentene side chain. On the basis of a comparison of the observed rotational band contours with that predicted by M05-2X/6-31+G* and CIS/6-31G calculations, firm assignments have been obtained for four of the five conformers, while the fifth is constrained to one of two possibilities. On the basis of values of three torsional angles along the pentene chain [about the C(α)−C(β) (τ1), C(β)−C(γ) (τ2), and C(γ)−C(δ) (τ3) bonds], the conformers can be uniquely labeled. By using this scheme, the assigned conformations are ggHγ′ for A, gaHγ′ for B, gaHγ for C, agHγ for D, and either aaHγ or agHγ′ for E. Single vibronic level fluorescence lifetimes have been recorded for a series of vibronic levels in the range 0−1500 cm−1 for all five conformers. A sharp drop in lifetime of all five conformers at ∼1000 cm−1 is proposed to accompany overcoming a rate-limiting barrier to exciplex formation.

Neutral serotonin−(H2O)n clusters with n = 1,2 have been studied under jet-cooled conditions using a combination of resonant two-photon ionization (R2PI), UV−UV hole-burning (UVHB), and resonant ion-dip infrared (RIDIR) spectroscopy. Serotonin (5-hydroxytryptamine, SERO) is a close analogue of tryptamine, differing by the addition of an OH substituent in the 5-position on the indole ring, but sharing the same ethylamine side chain in the 3-position. Three conformational isomers of SERO−(H2O)1 were observed via UVHB, with S0−S1 origins at 32 671 (A), 32 454 (B), and 32 188 cm−1 (C). RIDIR spectroscopy provided infrared spectra in the hydride stretch region that reflected the hydrogen-bonding arrangement of each conformer. Two of the three SERO−(H2O)1 conformers have RIDIR spectra nearly identical to that of the only observed conformer of tryptamine−(H2O)1, differing only in the orientation of the 5-OH group (syn vs anti). In this structure, the H2O molecule acts as H-bond donor to the NH2 group on the ethylamine side chain, which is configured in the Gpy(out) conformation that is the global minimum in the absence of water. Comparison of the OH stretch RIDIR spectrum of the third SERO−(H2O)1 conformer with calculation leads to its assignment to a structure in which the water molecule forms a H-bonded bridge between the amino group and the 5-OH group of SERO, with the ethylamine side chain in the Gph(out) conformation that facilitates bridge formation, corresponding to the second most populated conformer in the isolated SERO monomer. The OH and CH stretch infrared absorptions for the single observed conformer of SERO−(H2O)2 indicate that it is also a bridge structure linking the NH2 and OH groups of SERO, retaining the same Gph(out) ethylamine conformation as in conformer C of SERO−(H2O)1. The ultraviolet and infrared spectroscopy reflect the fact that the single-water bridge cannot optimally span the gap between the 5-OH and NH2 groups, while the water dimer bridge forms a set of three strong H-bonds that lock in the Gph(out) ethylamine and anti 5-OH orientations in a near-optimal configuration.

Stimulated emission pumping−population transfer spectroscopy (SEP-PTS) has been used to directly measure the energy threshold to isomerization between the two conformational isomers of bis(2-hydroxyphenyl)methane. These conformers have been shown in the preceding paper (DOI 10.1021/jp8098686) to be an OH···O H-bonded structure (conformer A) and a doubly OH ···π H-bonded conformer (conformer B). Lower and upper bounds on the energy threshold for A→B isomerization are at 1344 and 1399 cm−1, respectively, while the corresponding bounds on the B→A isomerization are 1413 and 1467 cm−1. The difference between these thresholds provides a measure of the relative energies of the two minima, with ΔEAB = EA − EB = 14−123 cm−1. The transition-state structure responsible for this energy threshold has been identified using DFT B3LYP, DFT M05-2X, and MP2 calculations, all with a 6-31+G* basis set. Only the DFT M05-2X calculations correctly reproduce both the energy ordering of the two minima and the magnitude of the barrier separating them. Below the energy threshold to isomerization, we have used the extensive Franck−Condon progressions present in the SEP spectrum of conformer A to undertake an SEP-PT study of its vibrational relaxation rate, as a function of internal energy over the 0−1200 cm−1 region. The position of SEP excitation in the expansion was systematically varied in order to change the rate and number of cooling collisions that occur between SEP excitation and probe steps and the initial temperature at which SEP occurs. From this data set, three energy regimes were identified, each with a unique value of the average energy lost per collision with helium (region 1: 13 cm−1/collision for E = 300−1200 cm−1, region 2: 0.6 cm−1/collision for E = 200−300 cm−1, and region 3: 7 cm−1/collision for E < 200 cm−1). In region 1, the vibrational density of states is sufficient to support efficient loss of energy via Δv = −1 collisions, involving the lowest-frequency vibrations of the molecule (with a frequency of 26 cm−1). In region 2, the vibrational energy levels are sufficiently sparse that energy gaps exist, reducing the efficiency of relaxation. In region 3, a combination of the quantum nature of the helium, attractive forces, and orbiting resonances may be responsible for the increased efficiency at lowest-energy regime.

Laser-induced fluorescence (LIF), ultraviolet hole-burning (UVHB), and resonant ion-dip infrared (RIDIR) spectroscopies were carried out on isolated benzo-15-crown-5 ether (B15C) and 4′-amino-benzo-15-crown-5 ether (ABC) cooled in a supersonic expansion. Three conformational isomers of B15C and four of ABC were observed and spectroscopically characterized. Full optimizations and harmonic frequency calculations were undertaken for the full set of almost 1700 conformational minima identified in a molecular mechanics force field search. When compared with TDDFT predictions, the S0−S1 origin positions serve as a useful diagnostic of the conformation of the crown ether near the phenyl ring responsible for the UV absorption and to the position of the NH2 substituent. In-plane orientations for the β carbons produce red-shifted S0−S1 origins, while out-of-plane “buckling” produces substantial blue shifts of 600 cm−1 or more. Comparison between the alkyl CH stretch spectra of B15C and ABC divide the spectra into common subgroups shared by the two molecules. The high-frequency CH stretch transitions (above 2930 cm−1) reflect the number of CH···O interactions, which in turn track in a general way the degree of buckling of the crown. On this basis, assignments of each of the observed conformational isomers to a class of structure can be made. All the observed structures have some degree of buckling to them, indicating that in the absence of a strong-binding partner, the crown folds in on itself to gain additional stabilization from weak dispersive and CH···O interactions.

Resonant two-photon ionization (R2PI), UV hole-burning (UVHB), and resonant ion-dip infrared (RIDIR) spectroscopy have been used to study the single-conformation infrared and ultraviolet spectroscopy of 3-(4-hydroxyphenyl)-N-benzylpropionamide (HNBPA, HOC6H5CH2CH2(C═O)NHCH2C6H5) cooled in a supersonic expansion. UVHB determines the presence of three conformers, two of which dominate the spectrum. RIDIR spectra in the OH stretch (3600−3700 cm−1), amide NH stretch (3450−3500 cm−1), and C═O stretch (1700−1750 cm−1) regions reveal the presence of small shifts in these fundamentals that are characteristic of the folding of the flexible chain and the ring−ring and ring−chain interactions. On the basis of a comparison of the experimental frequency shifts with calculations, the two major experimentally observed conformers are assigned to two folded structures in which the two aromatic rings are (nominally) face-to-face and perpendicular to one another. The perpendicular structure has a transition assignable to the S0−S2 origin, while the face-to-face structure does not, consistent with a faster nonradiative process in the latter case. The calculated structures and vibrational frequencies are quite sensitive to the level of theory due to the flexibility of the interconnecting chain and the importance of dispersive interactions between the two aromatic rings.

Near-pure samples of (E)-phenylvinylacetylene ((E)-PVA) and (Z)-phenylvinylacetylene ((Z)-PVA) were synthesized, and their ultraviolet spectroscopy was studied under jet-cooled conditions. The fluorescence excitation and UV−UV holeburning (UVHB) spectra of both isomers were recorded. The S0−S1 origin of (E)-PVA occurs at 33 578 cm−1, whereas that for (Z)-PVA occurs at 33 838 cm−1, 260 cm−1 above that for (E)-PVA. The present study focuses primary attention on the vibronic spectroscopy of (E)-PVA. Single vibronic level fluorescence spectra of many prominent bands in the first 1200 cm−1 of the S0−S1 excitation spectrum of (E)-PVA were recorded, including several hot bands involving low-frequency out-of-plane vibrations. Much of the ground-state vibronic structure observed in these spectra was assigned by comparison with styrene and trans-β-methylstyrene, assisted by calculations at the DFT B3LYP/6-311++G(d,p) level of theory. Both S0 and S1 states of (E)-PVA are shown to be planar, with intensity appearing only in even overtones of out-of-plane vibrations. Due to its longer conjugated side chain compared with that of its parent styrene, (E)-PVA supports extensive Duschinsky mixing among the four lowest-frequency out-of-plane modes (ν45−ν48), increasing the complexity of this mixing relative to that of styrene. Identification of the v′′ = 0−3 levels of ν48, the lowest frequency torsion, provided a means of determining the 1D torsional potential for hindered rotation about the Cph−Cvinyl bond. Vibronic transitions due to (Z)-PVA were first identified as small vibronic bands that did not appear in the UVHB spectrum recorded with the hole-burn laser fixed on the S0−S1 origin of (E)-PVA. The LIF and UVHB spectra of a synthesized sample of (Z)-PVA confirmed this assignment.

Abstract

The two-step laser excitation scheme of stimulated emission pumping (SEP) induces shifts of a single water molecule between two remote hydrogen bonding sites on trans-formanilide. This reaction can be initiated by selective excitation of either isomer (CO-bound or NH-bound) with different SEP excitation wavelengths. Energy (E) thresholds for isomerization in both directions have been measured [796 wave numbers ≤ E(CO→NH) ≤ 988 wave numbers and 750 wave numbers ≤ E(NH→CO) ≤ 988 wave numbers], and the energy difference DE between the CO-bound and NH-bound isomers was extracted (–238 wave numbers ≤ DE ≤ +192 wave numbers).

Abstract

Stimulated emission pumping (SEP)–hole filling spectroscopy and SEP-induced population transfer spectroscopy have been used to place narrow bounds on the energy thresholds for isomerization between individual reactant-product isomer pairs involving the seven conformational minima of tryptamine. The thresholds for isomerizing conformer A to all six other conformations divided into three groups at 750 wavenumbers (cm^–1)(A→B, F), 1000 cm^–1 [A→C(2)], and 1280 to 1320 cm^–1 [A→D, E, and C(1)]. The appearance of the first band and the absence of the band below it were used to place upper and lower bounds to the barrier heights for each process. The thresholds for A→B and B→A isomerizations were also combined to determine the relative energies of these two lowest energy minima. The combined data from all X→Y isomerizations identify important isomerization pathways on the potential energy surface linking the minima.

This paper describes further efforts to understand the excited state hydrogen atom dislocation of anthranilic acid. Resonant ion-dip infrared spectroscopy was used to probe the carbonyl stretch fundamental in both the ground and excited states in an effort to observe the excited state behavior of the heavy atoms surrounding the displaced hydrogen. A small peak in the excited state infrared spectrum was tentatively assigned to the carbonyl stretch fundamental, shifted 80 cm−1 to the red of its position in the ground state, indicative of a significant weakening of the CO bond. CASSCF calculations on a prototypical system, 3-amino-2-propenoic acid, were carried out to aid interpretation of vibrational frequencies and intensities. The effects of water complexation on the excited state hydrogen atom dislocation were also investigated. The vibronic spectrum, acquired by resonant two-photon ionization, displayed similar features as the monomer spectrum, as well as a progression in a low frequency intermolecular vibration. The infrared spectrum of the water complex, supported by density functional theory calculations, established that the water binds between the carbonyl oxygen and the acid hydrogen. The NH stretch fundamentals of the water complex in the ground and excited state were quite similar to those of the monomer, indicating complexation to water has little effect on the hydrogen atom dislocation

The conformational preferences of a series of capped peptides containing the helicogenic amino acid aminoisobutyric acid (Aib) (Z-Aib-OH, Z-(Aib)2-OMe, and Z-(Aib)4-OMe) are studied in the gas phase under expansion-cooled conditions. Aib oligomers are known to form 310-helical secondary structures in solution and in the solid phase. However, in the gas phase, accumulation of a macrodipole as the helix grows could inhibit helix stabilization. Implementing single-conformation IR spectroscopy in the NH stretch region, Z-Aib-OH and Z-(Aib)2-OMe are both observed to have minor conformations that exhibit dihedral angles consistent with the 310-helical portion of the Ramachandran map (ϕ, ψ = −57°, −30°), even though they lack sufficient backbone length to form 10-membered rings which are a hallmark of the developed 310-helix. For Z-(Aib)4-OMe three conformers are observed in the gas phase. Single-conformation infrared spectroscopy in both the NH stretch (Amide A) and CO stretch (Amide I) regions identifies the main conformer as an incipient 310-helix, having two free NH groups and two C10 H-bonded NH groups, labeled an F-F-10-10 structure, with a calculated dipole moment of 13.7 D. A second minor conformer has an infrared spectrum characteristic of an F-F-10-7 structure in which the third and fourth Aib residues have ϕ, ψ = 75°, −74° and −52°, 143°, Ramachandran angles which fall outside of the typical range for 310-helices, and a dipole moment that shrinks to 5.4 D. These results show Aib to be a 310-helix former in the gas phase at the earliest stages of oligomer growth.

Single-conformation ultraviolet and infrared spectroscopy was performed on dilignols containing two of the three biologically prevalent β-lignol linkages, erythro β–O–4 (β-aryl ether) and (±) β–β (pinoresinol). Both dilignols contain guaiacol(G)-type sub-units, representative of these linkages in G-type lignin. Resonant two-photon ionization (R2PI), IR-UV, and UV-UV holeburning (UVHB) spectroscopy in the cold, isolated environment of a supersonic expansion was carried out to determine the spectroscopic signatures associated with each linkage conformation, revealing striking differences in the vibronic intensity patterns between the two molecules in the UV. Two conformational isomers were found for the β–O–4 dilignol, both being classified into the fully hydrogen-bonded family with α-OH⋯OCH3 (C8) and γ-OH⋯Oβ (C5) H-bonds that are characteristic of the β–O–4 linkage. Conversely, a single dominant conformation was found for the conformationally-constrained pinoresinol. Resonant ion-dip infrared (RIDIR) spectroscopy provided conformation-specific IR spectra in the OH stretch and alkyl CH stretch regions, yielding complementary data that reported on both the intramolecular H-bonding and more subtle linkage features, respectively. DFT M05-2X calculations predict that the rigid β–β linkage had far fewer low-energy conformations in the first 20 kJ mol−1 (3) than the more flexible β–O–4 linkage (45). In the β–O–4 lignin dimer, the distinct UV chromophores lead to a splitting between S1 and S2 states that is determined mainly by the differences in the chemical structures of the two chromophores. In pinoresinol however, the assigned structure has C2 symmetry, with a calculated vertical excitonic splitting between the S1 and S2 states of 74 cm−1 (TDDFT). After taking into account the reduction in splitting associated with the geometry change in the aromatic rings upon electronic excitation, a vibronically quenched excitonic splitting of no more than a few wavenumbers is predicted for the C2 symmetric pinoresinol, but a definite experimental confirmation was not possible. These results predict that, under most circumstances, adjacent chromophores along a lignin polymer chain are not significantly electronically coupled to one another, and can be treated largely as isolated chromophores.

Mass-selective two-color resonant two-photon ionization (2C-R2PI) spectra of two resonance stabilized radicals (RSRs), 1-phenylallyl and benzylallenyl radicals, have been recorded under jet-cooled conditions. These two radicals, while sharing the same radical conjugation, have unique properties. The D0–D1 origin of the 1-phenylallyl radical is at 19208 cm−1, with extensive vibronic structure extending over 2000 cm−1 above the D1 origin. Much of this structure is assigned based on comparison with DFT and TDDFT calculations. Two-color photoionization efficiency scans reveal a sharp ionization threshold, providing a precise adiabatic ionization potential for the radical of 6.905(2) eV. By comparison, the benzylallenyl radical has an electronic origin at 19703 cm−1 and Franck–Condon activity similar to phenylallyl. The photoionization efficiency curve shows a gradual onset with apparent threshold at ∼7.50(2) eV. Visible–visible holeburning was used to show that each radical exists in one isomeric form in the expansion. The CH stretch IR spectrum of each radical was taken using D0-resonant ion dip infrared spectroscopy (D0-RIDIRS) in a novel four-laser experiment. Comparison of the IR spectrum with the predictions of DFT B3LYP calculations leads to firm assignment of each radical as the trans isomer. TDDFT calculations on the excited states of benzylallenyl suggest the possibility that the excited state levels originally excited convert to an all-planar form prior to ionization. The potential role that these radicals could play in Titan's atmosphere as intermediates in formation pathways for polycyclic aromatic hydrocarbons (PAHs) is briefly discussed.

The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

Laser induced fluorescence (LIF) excitation scans and dispersed fluorescence (DFL) spectra have been recorded for two four-carbon α,ω-diphenyl systems, diphenyldiacetylene (DPDA, ϕ-CC–CC-ϕ) and trans-diphenylvinylacetylene (DPVA, ϕ-CHCH–CC-ϕ) as isolated molecules cooled in a supersonic expansion. While these molecules have similar conjugation length, they exhibit strikingly different vibronic spectroscopy and photophysics. The near-UV LIF excitation spectrum of diphenyldiacetylene has its electronic origin at 32158 cm−1, and a strong progression in the CC stretch (2156 cm−1). All transitions are inherently broad, with widths of ∼30 cm−1 fwhm or greater. The S1 origin DFL spectrum is composed of sharp transitions with Franck–Condon activity mirroring that in the excitation spectrum, and broad emission shifted well to the red ascribable to phosphorescence on the μs timescale. Using ab initio calculations, it is possible to show that DPDA exists as a single, planar conformer with D2h symmetry. In contrast, trans-diphenylvinylacetylene shows intense sharp transitions in both LIF and DFL spectra with an S0–S1 origin of 31183.2 cm−1 and long progressions involving the in-plane fundamentals ν53 (bridge-phenyl bending) and ν51 (bridge-phenyl stretch). A sharp reduction in fluorescence yield in DPVA occurs within 300 cm−1 of the S1 origin. Possible causes for the photophysical processes occurring in the two molecules are discussed.

The ultraviolet spectroscopy of the S1← S0 transition of 1-phenylcyclopentene (PCP) was studied by resonant-two-photon ionization (R2PI), laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF). UV–UV hole-burning (UVHB) spectroscopy was used to determine that there is only one spectroscopically distinct conformer in the supersonic expansion. The excitation spectrum shows extensive vibronic structure extending to over 1000 cm−1 above the electronic origin (34646 cm−1). Much of the vibronic structure is similar to that of styrene and other singly substituted benzene derivatives, with Franck–Condon (FC) activity predominantly in substituent-sensitive benzene modes. Sizeable FC progressions were also found in the inter-ring torsion, reflecting a large displacement in the inter-ring angle upon electronic excitation. No evidence for FC activity in the ring-puckering coordinate is observed. The torsional potentials of the ground and excited states were determined from the experimental transition frequencies by fitting the calculated to the experimental torsional frequency spacings in an automated least-squares fitting procedure. The S1 torsional potential is a symmetric single-well potential centered around a locally planar equilibrium geometry at a torsional angle of ϕ = 0°. The energy levels are reproduced by a cosine term potential function with torsional parameters V2 = 3765 cm−1 and V4 = −183 cm−1. The S0 torsional potential possesses a twisted equilibrium geometry that is strongly asymmetric about ϕ = 0° due to the non-planarity of the cyclopentene ring. The best-fit potential parameters uses a sin/cos potential function (odd/even), with Ve2 = 948 cm−1, Ve4 = −195 cm−1, Vo2 = −162 cm−1 and Vo4 = −268 cm−1. The shape of the potentials are similar to those predicted by relaxed potential energy scans calculated at the DFT, CIS and TDDFT//CIS levels of theory. The change in the torsional angle ϕ upon electronic excitation was determined to be ∼15° from fits of the displacement δ of the S0 torsional potential with respect to the S1 potential. The simulated shift of the S0 potential with respect to the S1 potential of ∼15° is in very good agreement with that obtained from B3LYP calculations.

The vibronic excitation spectrum of phenylcyclopenta-1,3-diene (PCP3D) has been recorded in a supersonic expansion using resonant-two-photon ionization (R2PI) and laser-induced fluorescence (LIF) techniques. The spectrum is dominated by the S0–S1 origin transition (31739 cm−1), with several low-frequency vibronic bands in the first 400 cm−1, followed by a sharp cut-off in intensity due to turn-on of a non-radiative process. Single vibronic level fluorescence (SVLF) spectra were recorded for the S1 origin and several vibronic bands of PCP3D. The excitation and emission spectra show that the molecule is planar with Cs symmetry in both the ground and excited states. Torsional potentials were simulated from the observed torsional structure in the excitation and emission spectra. The S0 potential (V2 = 1237 cm−1, V4 = −256 cm−1) is associated with a flat-bottomed potential supporting large inter-ring angular changes with little cost in energy (±36° at 200 cm−1), with a barrier of 1237 cm−1 at the perpendicular geometry. The S1 potential is much stiffer about the planar geometry, with a calculated barrier five times larger than in S0 (V2 = 6732 cm−1, V4 = −477 cm−1). Based on the torsional assignments, weak bands in the same frequency region assigned earlier to the structural isomer phenylcyclopenta-1,4-diene [J. J. Newby, J. A. Stearns, C. P. Liu and T. S. Zwier, J. Phys. Chem. A, 2007, 111, 10914–10927] have been re-assigned as hot bands arising from v″ = 1 in the inter-ring torsion, ν57.

The conformational preferences of pentyl- through decylbenzene are studied under jet-cooled conditions in the gas phase. Laser-induced fluorescence excitation spectra, fluorescence-dip infrared spectra in the alkyl CH stretch region, and Raman spectra are combined to provide assignments for the observed conformers. Density functional theory calculations at the B3LYP-D3BJ/def2TZVP level of theory provide relative energies and normal mode vibrations that serve as inputs for an anharmonic local mode theory introduced in earlier work on alkylbenzenes with n = 2–4. This model explicitly includes anharmonic mixing of the CH stretch modes with the overtones of scissors/bend modes of the CH2 and CH3 groups in the alkyl chain, and is used to assign and interpret the single-conformation IR spectra. In octylbenzene, a pair of LIF transitions shifted −92 and −78 cm−1 from the all-trans electronic origin have unique alkyl CH stretch transitions that are fit by the local model to a g1g3g4 conformation in which the alkyl chain folds back over the aromatic ring π cloud. Its calculated energy is only 1.0 kJ mol−1 above the all-trans global minimum. This fold is at an alkyl chain length less than half that of the pure alkanes (n = 18), consistent with a smaller energy cost for the g1 dihedral and the increased dispersive interaction of the chain with the π cloud. Local site frequencies for the entire set of conformers from the local mode model show ‘edge effects’ that raise the site frequencies of CH2(1) and CH2(2) due to the phenyl ring and CH2(n − 1) due to the methyl group. The g1g3g4 conformer also shows local sites shifted up in frequency at CH2(3) and CH2(6) due to interaction with the π cloud.