Chien-Chih Chiang

Satellite hole investigations of the hole-burning mechanismand vibrational mode coupling of 9-aminoacridine doped inglycerol–water glasses at different pH values

The vibrational modes of the excited electronic state of 9-aminoacridine (9-AA) doped in amorphous glasses of glycerol and water mixtures have been examined via the satellite holes in the persistent hole-burned spectra. The satellite holes with high resolution were used to characterize tautomer structures of 9-AA at different pH values and provide information on the vibrationalmode coupling for the study of guest–host interactions. More fundamental modes were observed for monoprotonated 9-AA, butstronger couplings among the 390, 1162, and 1338 cm -1 modes are reflected in the combination modes for neutral 9-AA. Normal mode calculations of vibrational frequencies were performed to help mode assignments. Deuteriation of the amino group protons is carried out to distinguish between the vibrational modes of the acridine ring and the amino group. Franck–Condon factors were obtained from hole-burned spectra to assist in understanding the intensity distributions of the burned holes. Proton transfer between the chromophore and matrix, triggered by charge density migration along the short axis of 9-AA via electronic excitation, is proposed for the hole-burning mechanism.

Thermal recovery of spectral holes of dye molecules in polymer films. Site distribution in two-level systems

Abstract We have measured the temperature-annealing and the temperature-cycling hole-burning spectra of 5-(and 6-)carboxy-X-rhodamine-N-hydroxy-succinimidyl ester doped in polyvinyl alcohol films. The difference of the reduction of zero-phonon hole between annealing and cycling spectra can be described by the linear electron—phonon coupling, which provides the information of site distribution of asymmetric energy.

Investigation of guanine-rich DNA telomeric structure by a covalently linked BODIPY dye

We have investigated the interactions and structures of various guanine-rich oligonucleotides that are covalently linked by a BODIPY dye at the 5′ end. HPLC was used to purify and separate different complexes. A single predominant complex is collected for BODIPY-modified d(T10) and d(G10), while two major complexes are collected at different retention times for the BODIPY-modified d(CGCGT4CGCG) and d(T2G4T2G4) in the HPLC chromatograms during sample preparation. Distinct nonresonant holes in the satellite hole spectra allow us to distinguish different conformational structures with the same BODIPY–oligonucleotide sequence. In addition, our satellite hole results indicate that the coupling between the BODIPY and the thymine residues in the G-rich sequences can affect the yield of the G-rich aggregation. Furthermore, the appearance of new bands in the absorption spectra resulting from BODIPY aggregates may be a useful diagnostic of various G-rich structures at room temperature. This is because the BODIPY aggregates are driven by the association of G-rich sequences.

PHOTOREACTION OF NEUTRAL 9-AMINOACRIDINE IN GLYCEROL:WATER GLASS CHARACTERIZED BY SATELLITE HOLES AND ANTIHOLES

Abstract Satellite holes and antiholes in the hole burned (HB) spectrum are used to determine the photoproduct of 9-aminoacridine (9AA) doped in glycerol:water (Gl:H 2 O) glass with pH = 13. Although monoprotonated 9AA is the photoproduct of the imino form of neutral 9AA, antihole recovery implies that the excited state 9AA returns to original form of 9AA predominantly. Furthermore, similar satellite holes but different antihole structures are observed in the HB spectrum of 9AA doped in polyvinyl butyral film, implying that different HB mechanisms are involved.

Investigation of tautomeric structures of thionin by satellite holes: matrix dependence

Abstract We have applied the satellite hole spectroscopy to study the tautomeric structures of thionin dye in glycerol:water glass. Slightly different frequencies (∼15 cm −1 ) are observed for several satellite holes of thionin upon tuning the burning wavelength, implying that two conformational structures exist. However, only one set of satellite holes occurring in the spectrum of thionin doped in polyvinyl butyral film allows us to investigate the tautomeric structures of thionin in different matrices. Our results suggest that the appearance of two tautomeric structures of thionin in glycerol:water glass is due to the proton exchange between different sites of thionin and the matrix through intermolecular hydrogen bond.

Satellite hole investigation of binding mechanism of dipyrrometheneboron difluoride derivative and oligonucleotide in glycerol–water glass

The satellite holes in hole burned (HB) spectra have been used to study the binding modes of chromophore–oligonucleotide interactions. Substantial differences of several distinct satellite holes of 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succinimidyl ester (BODIPY591) chemically bound to an oligonucleotide of ten bases ofthymidine deoxyribonucleotides, d(T10), doped in glycerol–water (Gl–H2O) glass are observed. Normal mode calculations fordipyrrometheneboron difluoride (BODIPY) and an HB study of the BODIPY591 derivative have been conducted to help with vibrational mode assignments. The lack of appreciable perturbations on the vibrations of the diene chain and the phenyl group implies that these groups are much less perturbed upon interacting with d(T10). However, significant frequency differences for several N2BF2 modes indicate that the geometry of the N2BF2 moiety is dramatically perturbed upon interacting with d(T10). Our results suggest that the central ring of the BODIPY moiety is the main binding site and the electrostatic interaction between the BF2 group of BODIPY591 and the NH group of d(T10), as well as the stacking of the aromatic rings between BODIPY and thymine, are the most probable binding mechanisms.

Hole-Burning Structure and Mechanism of Acridine and Aminoacridines Doped in Polyvinyl Alcohol Films

Abstract Persistent hole-burning spectra of protonated acridine, 9-aminoacridine and proflavine doped in polyvinyl alcohol films have been studied to examine how the functional group affects chromophore-glass interactions. Proton transfer between the chromophore and the matrix upon electronic excitation is proposed to be the mechanism for the hole burned spectra of the three molecules studied. The high resolution of the spectrum of 9-aminoacridine is attributed to reduction of the electron-phonon coupling strength when substituting an amino group to the C(9) position of acridine. However, when substituting two amino groups to the C(3) and C(6) positions of acridine, significant increase of the electron-phonon coupling strength decreases the spectral resolution of proflavine.

Satellite holes of dye molecules doped in polymer films: intermolecular hydrogen-bond effect

Abstract We have studied the nonphotochemical hole-burned spectra of dye molecules in polyvinyl alcohol films, where the dye molecule contains a BF 2 functional group. An intense satellite hole that possibly corresponds to B-F bending is observed. The excitation into the B-F vibronic transition makes the rearrangement of the configurations of the host more efficient via the intermolecular hydrogen bond. In addition, temperature-annealing-cycling results show that the same magnitude of the electron-phonon coupling determines the electronic zero phonon hole (ZPH) and the vibronic satellite hole (SH), even in the presence of the intermolecular hydrogen bond. The hole intensity ratio of the SH to the ZPH suggests that the lowest absorption band consists of at least two prominent absorption components.

Temperature-annealing-cycling hole spectra of dye and dye-oligonucleotide doped in polymer films

Temperature-annealing-cycling hole spectra are introduced to examine the hole burning kinetics of dye and dye-oligonucleotide in polymer films. When a chromophore binds to a large group of oligonucleotide, the burning efficiency decreases and the electron-phonon coupling strength increases.

Investigation of telomeric DNA structures by a covalently linked BODIPY dye

Here we illustrate that nonresonant hole (NRH) spectroscopic method can be used to investigate the interactions and structures of various guanine-rich (G-rich) oligonucleotides that have made covalently linked by a dye of 4,4-difluoro-5-(4-phenyl- l,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succinimidyl ester (BODIPY) at the 5’ end. Telomeres, the ends of chromosomes, are essential for the stability and replication of eukaryotic chromosomes [1].