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

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

Single conformation spectroscopy of a flexible bichromophore: 3-(4-hydroxyphenyl)-N-benzylpropionamide

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, HOC6H 5CH2CH2(C=O)NHCH2C6H 5) 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. © 2008 American Chemical Society

Theoretical modeling of the OH stretch infrared spectrum of carboxylic acid dimers based on first-principles anharmonic couplings

A simple physical picture of the dominant cause for the unusual breadth and sub-structure of the O-H stretch infrared spectrum of carboxylic acid dimers was established. Cubic anharmonic constants were calculated for FAD and BAD using a set of five key internal coordinates

Direct measurement of the energy thresholds to conformational isomerization in Tryptamine: Experiment and theory

The methods of stimulated emission pumping-hole spectroscopy (SEP-HFS) and stimulated emission pumping population transfer spectroscopy (SEP-PTS) were applied to the conformation-specific study of conformational isomerization in tryptamine. The methods employ stimulated emission pumping to selectively excite a fraction of the population of a single conformation of TRA to well-defined ground-state vibration levels. The method uses collisions as an integral part of the experimental scheme. Hole-filling methods can also be applied to the study of isomerization in a much wider range of contexts

Resonant ion-dip infrared spectroscopy of the S<inf>4</inf> and D<inf>2d</inf> water octamers in benzene-(water)<inf>8</inf> and benzene<inf>2</inf>-(water)<inf>8</inf>

The techniques of resonant two-photon ionization (R2PI), UV-UV (ultraviolet) hole-burning, and resonant ion-dip infrared (RIDIR) spectroscopies have been employed along with density functional theory (DFT) calculations to assign and characterize the hydrogen-bonding topologies of two isomers each of the benzene-(water)8 and (benzene)2(water)8 gas-phase clusters. The BW8 isomers (B=benzene, W=water) have R2PI spectra which are nearly identical to one another, but shifted by about 5 cm-1 from one another. This difference is sufficient to enable interference-free RIDIR spectra to be recorded. As with smaller BWn clusters, the BW8 clusters fragment following photoionization by loss of either one or two water molecules. The OH stretch IR spectra of the two BW8 isomers bear a close resemblance to one another, but differ most noticeably in the double-donor OH stretch transitions near 3550 cm-1. Comparison to DFT calculated minimum energy structures, vibrational frequencies, and infrared intensities leads to an assignment of the H-bonding topology of the BW8 isomers as nominally cubic water octamers of S4 and D2d symmetry surface attached to benzene through a π H-bond. A series of arguments based on the R2PI and hole-burning spectra leads to an assignment of additional features in the R2PI spectra to two isomers of B2W8. The OH stretch RIDIR spectra of these isomers show them to be the corresponding S4 and D2d analogs of B2W8 in which the benzene molecules each form a π H-bond with a different dangling OH group on the W8 sub-cluster. © 1998 American Institute of Physics

Entropy-driven population distributions in a prototypical molecule with two flexible side chains: O -(2-acetamidoethyl)- N -acetyltyramine

Resonant two-photon ionization (R2PI), resonant ion-dip infrared (RIDIR), and UV-UV hole-burning spectroscopies have been employed to obtain conformation-specific infrared and ultraviolet spectra under supersonic expansion conditions for O -(2-acetamidoethyl)- N -acetyltyramine (OANAT), a doubly substituted aromatic in which amide-containing alkyl and alkoxy side chains are located in para positions on a phenyl ring. For comparison, three single-chain analogs were also studied: (i) N -phenethyl-acetamide (NPEA), (ii) N - (p -methoxyphenethyl-acetamide) (NMPEA), and (iii) N -(2-phenoxyethyl)- acetamide (NPOEA). Six conformations of OANAT have been resolved, with S0 - S1 origins ranging from 34 536 to 35 711 cm-1, denoted A-F, respectively. RIDIR spectra show that conformers A-C each possess an intense, broadened amide NH stretch fundamental shifted below 3400 cm-1, indicative of the presence of an interchain H bond, while conformers D-F have both amide NH stretch fundamentals in the 3480-3495 cm-1 region, consistent with independent-chain structures with two free NH groups. NPEA has a single conformer with S0 - S1 origin at 37 618 cm-1. NMPEA has three conformers, two that dominate the R2P1 spectrum, with origin transitions between 35 580 and 35 632 cm-1. Four conformations, one dominate and three minor, of NPOEA have been resolved with origins between 35 654 and 36 423 cm-1. To aid the making of conformational assignments, the geometries of low-lying structures of all four molecules have been optimized and the associated harmonic vibrational frequencies calculated using density functional theory (DFT) and RIMP2 methods. The S0 - S1 adiabatic excitation energies have been calculated using the RICC2 method and vertical excitation energies using single-point time-dependent DFT. The sensitivity of the S0 - S1 energy separation in OANAT and NPOEA primarily arises from different orientations of the chain attached to the phenoxy group. Using the results of the single-chain analogs, tentative assignments have been made for the observed conformers of OANAT. The RIMP2 calculations predict that interchain H-bonded conformers of OANAT are 25-30 kJmol more stable than the extended-chain structures. However, the free energies of the interchain H-bonded and extended structures calculated at the preexpansion temperature (450 K) differ by less than 10 kJmol, and the number of extended structures far outweighs the number of H-bonded conformers. This entropy-driven effect explains the presence of the independent-chain conformers in the expansion, and cautions future studies that rely solely on relative energies of conformers in considering possible assignments. © 2007 American Institute of Physics