Resonant Ion-dip Infrared Research Articles

Solvent Effects on the Conformational Preferences of Serotonin: Serotonin−(H2O)n, n = 1,2

Neutral serotonin-(H(2)O)(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-(H(2)O)(1) were observed via UVHB, with S(0)-S(1) 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-(H(2)O)(1) conformers have RIDIR spectra nearly identical to that of the only observed conformer of tryptamine-(H(2)O)(1), differing only in the orientation of the 5-OH group (syn vs anti). In this structure, the H(2)O molecule acts as H-bond donor to the NH(2) 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-(H(2)O)(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-(H(2)O)(2) indicate that it is also a bridge structure linking the NH(2) and OH groups of SERO, retaining the same Gph(out) ethylamine conformation as in conformer C of SERO-(H(2)O)(1). The ultraviolet and infrared spectroscopy reflect the fact that the single-water bridge cannot optimally span the gap between the 5-OH and NH(2) 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.

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, HOC6H5CH2CH2(CO)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 CO 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.

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 S(0)-S(1) 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 S(0)-S(1) 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 S(0)-S(1) adiabatic excitation energies have been calculated using the RICC2 method and vertical excitation energies using single-point time-dependent DFT. The sensitivity of the S(0)-S(1) 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 kJ/mol 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 kJ/mol, 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.

The Infrared and Ultraviolet Spectra of Individual Conformational Isomers of Biomolecules: Tryptamine

Resonant ion-dip infrared (RIDIR) and UV−UV hole-burning spectroscopies are used to record the hydride stretch infrared spectra and S1←S0 ultraviolet spectra of each of seven conformational isomers of tryptamine free from interference from one another. The different conformations of the ethylamine side chain produce unique S1←S0 vibronic spectra, which can serve as the basis for RIDIR spectroscopy. The seven conformers possess unique spectral signatures in the alkyl CH stretch region of the infrared, which aid in the assignment of the observed transitions in the ultraviolet. Density functional theory (DFT) calculations of the structures, relative energies, and harmonic vibrational frequencies of nine low-energy minima are compared with the present and previous experimental data on tryptamine to assign the spectra of all seven conformers, all of which point the α carbon out of the plane of the indole ring. The nine conformers consist of all combinations of the three minimum-energy amino group positions (an...

Resonant ion-dip infrared spectroscopy of benzene–(water)9: Expanding the cube

The techniques of resonant two-photon ionization (R2PI), UV-UV hole-burning, and resonant ion-dip infrared (RIDIR) spectroscopy have been employed along with density functional theory (DFT) calculations to characterize the hydrogen-bonding topologies of three isomers of benzene–(water)9. Isomers I and II, with R2PI transitions shifted, respectively, by +77 and +63 cm−1 from the benzene monomer, have similar intensities in the R2PI spectrum. The signal from the third isomer (isomer III, shifted +60 cm−1) is present at about one-fourth the intensity of the other two. The experimental RIDIR spectrum of isomer I bears a strong resemblance to the spectrum of the benzene–(water)8 D2d-symmetry cubic structure identified in earlier work, but possessing an extra single-donor transition associated with the ninth water molecule. Using the S4 and D2d symmetry forms of the water octamer as base structures to which the ninth water molecule can be added, a total of nine “expanded-cube” structures are identified for W9 arising from two distinct insertion points in the W8(D2d) cube (D1,D2) and three such points in the W8(S4) cube (S1-S3). DFT calculations predict these to be spread over an energy range of less than 1 kcal/mol. Given that each of the nine “expanded-cube” (water)9 structures contains five symmetry-inequivalent free OH groups, a total of 45 “expanded-cube” benzene–(water)9 conformational isomers are predicted. Structural and vibrational frequency calculations have been performed on seven of these to determine how the (water)9 structural type and the attachment point of benzene to the structure affect the total energy and vibrational frequencies of the cluster. Based on a comparison of the experimental RIDIR spectrum with the calculated vibrational frequencies and infrared intensities, isomer I is attributed to the BW9(D1) structure in which benzene attaches to W9(D1) at the free OH of the water molecule which donates a H-bond to the ninth water. This structure has a calculated binding energy that is about 0.13 kcal/mol greater in magnitude than any other benzene–(water)9 isomer studied. The experimental spectra of isomers II and III are of insufficient quality to assign them to specific BW9 structures with confidence. However, isomer II is most consistent with an S4-derived expanded cube structure (either S1 or S2), while isomer III shows characteristics consistent with a second D1-derived BW9 structure in which benzene is attached at a position on the expanded cube remote from the ninth water.

Resonant Ion-Dip Infrared Spectroscopy of Ternary Benzene−(Water)n(Methanol)m Hydrogen-Bonded Clusters

Resonant two-photon ionization, IR−UV 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-bonded topologies and structures of eight benzene−(H2O)n(CH3OH)m, cluster isomers (hereafter shortened to BWnMm) with n + m ≤ 4. The O−H stretch infrared fundamentals are used to determine the H-bonding topology of the clusters. However, in several cases, the O−H stretch spectrum leaves an ambiguity regarding the position of the methanols within the structure. In these cases, the methyl CH stretch region serves as a secondary probe capable of distinguishing among the various possibilities. For n + m = 2, a single BWM isomer is observed with OH stretch fundamentals at 3508, 3606, and 3718 cm-1. A comparison of the methyl CH stretch transitions of BWM and BM2 reveals that the methanol in BWM accepts a H-bond from water and forms a π H-bond with benzene. The n + m = 3 results show the subtle ...

Resonant ion-dip infrared spectroscopy of benzene–(water)n–(methanol)m clusters with n+m=4, 5

Resonant two-photon ionization and resonant ion-dip infrared (RIDIR) spectra of benzene–(water)n–(methanol)m clusters (hereafter shortened to BWnMm) have been recorded for a total of seven clusters with n+m=4 and 5. The infrared spectra in the OH and CH stretch regions show absorptions characteristic of H-bonded WnMm clusters which are bound to benzene by a π H-bond involving a dangling OH on the WnMm sub-unit. Density functional theory (DFT) calculations identify a number of conformational isomers in the n+m=4 series which meet the general criteria imposed by the experimental spectra. The structures, binding energies, harmonic vibrational frequencies, and infrared intensities for these isomers have been calculated for comparison with experiment. Based on the calculations, tentative assignments of several of the observed species are given. The calculations uncover the fact that complexation of benzene to the cyclic water tetramer imposes much the same perturbations on the cycle as substitution of methanol for water. In particular, the single-donor OH stretch spectra of WnMm and BWn+1Mm−1 are calculated to be virtually identical to one another. The comparison of experiment and theory for this series of cyclic structures is used to assess the strengths and limitations of the calculations at the DFT Becke3LYP/6-31+G* level of theory.

Resonant ion-dip infrared spectroscopy of the S4 and D2d water octamers in benzene-(water)8 and benzene2-(water)8

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.

Infrared Spectrum of a Molecular Ice Cube: The S 4 and D 2 d Water Octamers in Benzene-(Water) 8

Resonant two-photon ionization, ultraviolet hole-burning, and resonant ion-dip infrared (RIDIR) spectroscopy were used to assign and characterize the hydrogen-bonding topology of two conformers of the benzene-(water) 8 cluster. In both clusters, the eight water molecules form a hydrogen-bonded cube to which benzene is surface-attached. Comparison of the RIDIR spectra with density functional theory calculations is used to assign the two (water) 8 structures in benzene-(water) 8 as cubic octamers of D 2 d and S 4 symmetry, which differ in the configuration of the hydrogen bonds within the cube. OH stretch vibrational fundamentals near 3550 wave numbers provide unique spectral signatures for these “molecular ice cubes.”

The ultraviolet and infrared spectroscopy of (benzene) 2-(CH 3OH) 3 isomeric clusters

A combination of resonant two-photon ionization (R2PI), resonant ion-dip infrared (RIDIR) and infrared-ultraviolet (IR-UV) hole-burning spectroscopies has been used to distinguish, assign, and spectroscopically characterize an otherwise complicated, overlapping set of transitions which all appear in the benzene-(CH 3OH) 3 + mass channel ( m/ e = 174) in a one-color resonant two-photon ionization spectrum. Several of the previously unassigned transitions are here assigned to two conformational isomers of (benzene) 2-(CH 3OH) 3 clusters.