Infrared spectroscopy of gas phase alpha hydroxy carboxylic acid homo and hetero dimers.

New gas phase infrared spectroscopy is reported for an aromatic alpha hydroxy carboxylic acid homo dimer of 9-hydroxy-9-fluorene carboxylic acid (9HFCA)2, and the hetero dimer of 9HFCA with glycolic acid. In terms of the 9-hydroxy stretching frequency, the 16 cm-1 blue-shift in the homo dimer and the 17 cm-1 blue-shift in the hetero dimer, relative to that in 9HFCA monomer, are attributed to collective effects with anti-cooperativity stronger than cooperativity. Furthermore, for the hetero dimer, the two alpha hydroxy groups' stretching frequencies are clearly resolved, and differ by 30 cm-1. This difference represents a modest, quantitative enhancement of the intramolecular H-bond by the fluorene moiety in 9HFCA monomer, as opposed to that in glycolic acid. Accurate vibrational frequencies of the alpha OH, 3568 cm-1 in the bare glycolic acid, and 3584 cm-1 in the glycolic acid homo dimer are determined for the first time by comparison to 9HFCA monomer, homo and hetero dimers. The quantitative studies by infrared spectroscopy reveal subtle interactions among intra- and intermolecular H-bonds in the alpha hydroxyl acid dimers, which are also uniquely extended to probe each monomer's subtle intramolecular interactions.

Influences of the propyl group on the van der Waals structures of 4-propylaniline complexes with one and two argon atoms studied by electronic and cationic spectroscopy.

4-propylaniline complexes with one and two argon atoms formed in the molecular beam were studied in the first excited electronic state, S1, using resonance enhanced two-photon ionization spectroscopy and in the cation ground state, D0, using mass analyzed threshold ionization spectroscopy. The combination of electronic and cationic spectra of the clusters allows two conformations to be identified in both aniline-Ar1 and aniline-Ar2, which are assigned to either the gauche configuration or anti-configuration of 4-propylaniline. The gauche isomer exhibits complex bands shifted 29 cm(-1) and 89 cm(-1) from the S1 origin bands and 83 cm(-1) and 148 cm(-1) from the ionization potential assigned to the Ar1 and Ar2 complexes, respectively. For the anti-rotamer, the corresponding shifts actually become nearly additive, 53 cm(-1) and 109 cm(-1) for the S1 origin bands, and 61 cm(-1) and 125 cm(-1) for the ionization potentials. Ab initio calculations provide insights into the influences of the propyl and amino groups on the positions of the argon atoms within the clusters. In addition, the binding energy of one argon with the gauche isomer of 4-propylaniline has been measured to be 550 ± 5 cm(-1) in the D0 state, 496 ± 5 cm(-1) in the S1 state, and 467 ± 5 cm(-1) in the neutral ground state, S0.

Electronic and cationic spectroscopy of 9-hydroxy-9-fluorene carboxylic acid.

Resonance-enhanced multiphoton ionization spectroscopy of supersonically cooled gas-phase 9-hydroxy-9-fluorene carboxylic acid (9HFCA) is reported for its first electronic excited state, S1. The UV-UV hole-burning experiment identifies a single conformer in the molecular beam, stabilized by an intramolecular hydrogen bond. For this Cs symmetric conformer, two low frequencies in the S1 spectrum are assigned: an in-plane rocking mode of the carboxylic acid side chain lies at 58 cm(-1), and an in-plane fluorene bending mode appears at 183 cm(-1). The corresponding mode frequencies in the cation, 58 and 196 cm(-1), are measured by zero electron kinetic energy (ZEKE) spectroscopy upon pumping the S1 vibronic states. The adiabatic ionization potential is measured to be 64 923 ± 5 cm(-1). In addition, a feature established by ZEKE spectroscopy upon pumping the hot band is found at 67 cm(-1). This is assigned as a hot band of the HO-C9-COOH rocking mode in the neutral ground state.

Communication: The ionization spectroscopy of mixed carboxylic acid dimers.

We report mass analyzed threshold ionization spectroscopy of supersonically cooled gas phase carboxylic complexes with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. The vibrationally resolved cation spectrum for the 9HFCA complex with formic acid allows accurate determination of its ionization potential (IP), 64,374 ± 8 cm(-1). This is 545 cm(-1) smaller than the IP of 9HFCA monomer. The IPs of 9HFCA complexes with acetic acid and benzoic acid shift by -1133 cm(-1) and -1438 cm(-1), respectively. Density functional calculations confirm that Cs symmetry is maintained upon ionization of the 9HFCA monomer and its acid complexes, in contrast to the drastic geometric rearrangement attending ionization in complexes of 9-fluorene carboxylic acid. We suggest that the marginal geometry changes and small IP shifts are primarily due to the collective interactions among one intramolecular and two intermolecular hydrogen bonds in the dimer.

Zero kinetic energy photoelectron spectroscopy of tryptamine and the dissociation pathway of the singly hydrated cation cluster.

The relative ionization energies of tryptamine conformations are determined by zero kinetic energy photoelectron spectroscopy and photoionization efficiency measurements. The relative cationic conformational stabilities are compared to the published results for the neutral molecule. In the cation, the interaction strength changes significantly between amino group and either the phenyl or the pyrrole moiety of the indole chromophore where most of the positive charge is located, leading to different conformational structures and relative conformer energies in the cation. In particular, the measured adiabatic ionization potential of isomer B is 60,928 ± 5 cm(-1), at least 400 cm(-1) higher than any of the 6 other tryptamine isomers which all have ionization potentials within 200 cm(-1) of each other. In addition to the monomer, measurements were made on the A conformer of the tryptamine(+)-H(2)O complex including the ionization threshold and cation dissociation energy measured using a threshold photoionization fragmentation method. The water cluster exhibits an unexpectedly high ionization potential of 60,307 ± 100 cm(-1), close to the conformer A monomer of 60 320 ± 100 cm(-1). It also exhibits surprisingly low dissociation energy of 1750 ± 150 cm(-1) compared to other H-bonding involved cation-H(2)O complexes which are typically several thousands of wavenumbers higher. Quantum chemical calculations indicate that upon ionization the structure of the parent molecule in the water complex remains mostly unchanged due to the rigid intermolecular double hydrogen bonded water molecule bridging the monomer backbone and its side chain thus leading to the high ionization potential in the water cluster. The surprisingly low dissociation energy measured in the cationic water complex is attributed to the formation of a much more stable structural isomer H(+) in the exit channel.

Communication: spectroscopic measurement of the binding energy of a carboxylic acid-water dimer.

Infrared-ultraviolet two color pump-probe spectroscopy is used to measure the binding energy, D(0,) of a carboxylic acid-water dimer where the acid is 9-hydroxy-9-fluorenecarboxylic acid. The acid-water configuration presents a standard structure for the general acid-water interaction where the water bonds to the carboxylic acid group through two intermolecular hydrogen bonds. Photodissociation studies with product vibrational state resolution have enabled an accurate determination of the binding energy for this acid-water system to be D(0) = 2975 ± 30 cm(-1). Quantum chemical calculations are performed to compare with the experimental observations and a recent measurement on the water dimer (D(0) = 1105 ± 10 cm(-1)).

Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths.

Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

Cation spectroscopy and binding energy determination for 1,4-benzodioxan-Ar1 and -Ar2 complexes.

Cation vibronic spectra are measured for 1,4-benzodioxan (BZD) and van der Waals complexes of BZD with one and two Ar atoms using zero electron kinetic energy and mass analyzed threshold ionization spectroscopy. The spectra of the monomer cation were used to measure the frequencies of the two key low-frequency modes which had previously been extensively studied in the neutral S0 and S1 states. The aliphatic ring twisting mode, nu25, has an energy of 146 cm(-1) in the cation, intermediate between the values found in the S0 and S1 states. The bending, butterfly-like mode nu48 has an energy of 125 cm(-1), which is of higher frequency than either of the neutral states. The S1 spectra of the BZD-Ar1 and BZD-Ar2 complexes are recorded and observed to have modest red shifts from the monomer. The cation spectra of the complexes are also measured using mass analyzed threshold ionization spectroscopy including scans at higher energy which are used to determine the Ar binding energies. The energies for the loss of one Ar atom were determined to be 630 +/- 10 and 650 +/- 10 cm(-1) for BZD-Ar and BZD-Ar2, respectively. The similar cation spectra and similar binding energies indicate that each Ar atom in BZD-Ar2 has a similar binding geometry. Quantum chemical calculations were performed which had fair agreement with the measured binding energies and give some insight into the specific binding geometry.

Photophysical Characterization of Enhanced 6-Methylisoxanthopterin Fluorescence in Duplex DNA.

The structure and dynamic motions of bases in DNA duplexes and other constructs are important for understanding mechanisms of selectivity and recognition of DNA-binding proteins. The fluorescent guanine analogue, 6-methylisoxanthopterin 6-MI, is well suited to this purpose as it exhibits an unexpected 3- to 4-fold increase in relative quantum yield upon duplex formation when incorporated into the following sequences: ATFAA, AAFTA, or ATFTA (where F represents 6-MI). To better understand some of the factors leading to the 6-MI fluorescence increase upon duplex formation, we characterized the effect of local sequence and structural perturbations on 6-MI photophysics through temperature melts, quantum yield measurements, fluorescence quenching assays, and fluorescence lifetime measurements. By examining 21 sequences we have determined that the duplex-enhanced fluorescence (DEF) depends on the composition of bases adjacent to 6-MI and the presence of adenines at locations n ± 2 from the probe. Investigation of duplex stability and local solvent accessibility measurements support a model in which the DEF arises from a constrained geometry of 6-MI in the duplex, which remains H-bonded to cytosine, stacked with adjacent bases and inaccessible to quenchers. Perturbation of DNA structure through the introduction of an unpaired base 3' to 6-MI or a mismatched basepair increases 6-MI dynamic motion leading to fluorescence quenching and a reduction in quantum yield. Molecular dynamics simulations suggest the enhanced fluorescence results from a greater degree of twist at the X-F step relative to the quenched duplexes examined. These results point to a model where adenine residues located at n ± 2 from 6-MI induce a structural geometry with greater twist in the duplex that hinders local motion reducing dynamic quenching and producing an increase in 6-MI fluorescence.

Binding energies and dissociation pathways in the aniline-Ar2 cation complex.

Mass analyzed threshold ionization spectroscopy is used to measure the Ar binding energy for the cationic aniline-Ar (An(+)-Ar) and aniline-Ar(2) (An(+)-Ar(2)) complexes. Since the experiments begin with the neutral species, photoexcitation creates the cations in the pi-bonding configuration with the Ar located above the phenyl ring. The binding energy in this conformation of the An(+)-Ar complex is determined to be 495+/-15 cm(-1). Measurements of An(+)-Ar(2) revealed the production of a lower energy dissociation product which is assigned to the An(+)-Ar H-bonding configuration. Combinations of measurements allow determination of the dissociation energy of this complex to be 640+/-20 cm(-1). The observation of a more stable H-bonded conformer is consistent with recent infrared experiments on An(+)-Ar complexes created by complexing An(+) with Ar, rather than creation through the neutral complex. Calculations are presented which closely reproduce the binding energy of the pi bound Ar but underestimate the stability of the H-bonded species.

Tryptophol cation conformations studied with ZEKE spectroscopy.

The relative energies of several conformations of the tryptophol cation are determined by zero kinetic energy (ZEKE) photoelectron spectroscopy and photoionization efficiency measurements. Recently published high-resolution electronic spectroscopy on the neutral species determined the absolute configuration of the different conformers in the S1 spectrum. These assignments are utilized in the photoelectron experiments by pumping through conformer specific S1 resonances yielding ZEKE spectra of the specific, assigned conformations. The adiabatic ionization of one specific conformation is definitively determined, and two others are estimated. The photoelectron spectra, coupled with calculations, reveal that structural changes upon ionization are dominated by interactions of the hydroxyl group with the changes of electronic structure in the aromatic system.

Vibrational dynamics of 9-fluorenemethanol using infrared-ultraviolet double-resonance spectroscopy.

Vibrational spectroscopy of jet-cooled 9-fluorenemethanol and its clusters 9-fluorenemethanol-H2O, 9-fluorenemethanol-CH3OH, 9-fluorenemethanol-C2H5OH, and 9-fluorenemethanol-C3H7OH has been carried out using an IR-UV double-resonance method. The spectrum of the OH stretching vibration, v(OH), has been measured for the 9-fluorenemethanol monomer and for each of the clusters. Two conformers of 9-fluorenemethanol, symmetric (sym) and unsymmetric (unsym), have been identified using a combination of spectroscopy and quantum chemical calculations with B3LYP and HF methods using the 6-31G(d) basis set. Vibrational dynamics resulting from IR excitation has also been studied using the S0-S1 transition probed by a nanosecond-time-delayed UV laser. The data suggest that isomerization occurs as a result of the IR excitation, but the breadth of the probe spectra makes an unequivocal conclusion difficult. The effect of hydrogen bonding on the v(OH) of 9-fluorenemethanol has also been studied in clusters with water, methanol, ethanol, and propanol by measuring the IR spectra. Cluster dissociation dynamics have also been studied following IR excitation. It is observed that upon excitation of the cluster of a particular conformation the monomer product is generally produced in both conformer forms. Energetic considerations indicate that isomerization occurs before dissociation.