Mattanjah S. de Vries

Vibrational Raman and infrared spectra of chromatographically separated C60 and C70 fullerene clusters

Abstract We report vibrational Raman and infrared spectra for chemically separated C 60 and C 70 fullerenes. Thin film samples were prepared by subliming the chromatographically separated species onto appropriate substrates. The C 60 Raman spectrum shows eight clear lines and two weaker ones. If C 60 in fact that has the proposed buckminsterfullerene structure (as is strongly indicated by recent experiments), the present Raman measurements together with the four observed IR frequencies give a complete set of Raman and infrared active fundamental frequencies for this molecule. A comparison of this set with the calculated spectrum for buckminsterfullerene shows satisfactory agreement.

Pairing of isolated nucleic-acid bases in the absence of the DNA backbone

The two intertwined strands of DNA are held together through base pairing—the formation of hydrogen bonds between bases located opposite each other on the two strands. DNA replication and transcription involve the breaking and re-forming of these hydrogen bonds, but it is difficult to probe these processes directly. For example, conventional DNA spectroscopy is dominated by solvent interactions, crystal modes and collective modes of the DNA backbone; gas-phase studies, in contrast, can in principle measure interactions between individual molecules in the absence of external effects, but require the vaporization of the interacting species without thermal degradation. Here we report the generation of gas-phase complexes comprising paired bases, and the spectroscopic characterization of the hydrogen bonding in isolated guanine–cytosine (G–C) and guanine–guanine (G–G) base pairs. We find that the gas-phase G–C base pair adopts a single configuration, which may be Watson–Crick, whereas G–G exists in two different configurations, and we see evidence for proton transfer in the G–C pair, an important step in radiation-induced DNA damage pathways. Interactions between different bases and between bases and water molecules can also be characterized by our approach, providing stringent tests for high-level ab initio computations that aim to elucidate the fundamental aspects of nucleotide interactions.

Scandium clusters in fullerene cages.

The production and spectroscopic characterization of fullerene-encapsulated metal-atom clusters is reported. In particular, both solution and solid-state electron paramagnetic resonance (EPR) spectra of Sc3C82 have been obtained. ScC82 also gives an EPR spectrum, but Sc2Cn species—the most abundant metallofullerenes in the mass spectrum—are EPR-silent even though Sc2 is EPR-active in a rare-gas matrix at 4.2 K. The results suggest that the three scandium atoms in Sc3C82 form an equilateral triangle—as was previously suggested for Sc3 molecules isolated in a cryogenic rare-gas matrix. The spectrum of ScC82 has features similar to those found earlier for LaC82 and YC82, suggesting that it can also be described as a +3 metal cation within a -3 fullerene radical anion. An implication of this work is that production of macroscopic quantities of clustercontaining fullerenes may make possible the fabrication of exotic new structures with regular arrays of metal-atom clusters isolated in fullerene molecules, resulting in a new type of host/guest nanostructured material.

Excited state dynamics of DNA bases

Biochemical reactions are subject to the particular environmental conditions of planet earth, including solar irradiation. How DNA responds to radiation is relevant to human health because radiation damage can affect genetic propagation and lead to cancer and is also important for our understanding of how life on earth developed. A reductionist approach to unravelling the detailed photochemistry seeks to establish intrinsic properties of individual DNA building blocks, followed by extrapolation to larger systems, to incorporate interactions between the building blocks and the role of the biomolecular environment. Advances in both experimental and computational techniques have lead to increasingly detailed insights in the excited state dynamics of DNA bases in isolation as well as the role of the solvent and intermolecular interactions. This review seeks to summarise current findings and understanding.

REMPI Spectroscopy of Laser Desorbed Guanosines

To observe fundamental properties of DNA building blocks it is desirable to study individual nucleosides in the gas phase without interference from solvent molecules, or macromolecular structure. As a first step, we have recently reported the first vibronic spectrum of the nucleobase guanine, obtained by a combination of laser desorption, jet cooling, and resonance enhanced multiphoton ionization (REMPI).1 Although guanine is important as a chromophore in DNA, it is more realistic for understanding the photochemistry of DNA to study the nucleosides. Those are even harder to vaporize intact because they are thermally more labile and, with their larger molecular weights, have still lower vapor pressures. Using laser desorption, we have now succeeded in forming a molecular beam of nucleosides, and we report the first REMPI spectra of a series of individual guanosines, namely guanosine (Gs), 2′deoxyguanosine (2′deoxyGs), and 3′deoxyguanosine (3′deoxyGs). We compare our results with computations at the HF 6-31G(d,p) level. The results suggest the occurrence of two different conformations, each probably stabilized by internal hydrogen bonds. One of those two conformations is absent in 2′deoxyGs implying that the 2′ hydroxyl group is required for its stabilization. Spectroscopic properties of guanosines have been studied primarily by Raman techniques in solution.2-9 A great deal of attention has been given to potential Raman markers for hydrogen bonding and for structural conformation. Observation of hydrogen bonding by Raman spectroscopy requires identification of vibrations that depend strongly on those specific atoms in guanine, that serve as either proton donor or acceptor. However, most vibrations involve the concerted motion of multiple atoms, and therefore correlation of marker frequencies with specific hydrogen bonding sites is not straightforward. Guanosine vibrations involving motion along the glycosidic bond may provide conformational markers if their frequencies are sensitive to puckering of the ribose ring or for rotation around the sugar-base bond. Interpretation of these markers requires careful analysis of complex vibrational modes. On the other hand, different conformations can be observed much more directly by vibronic spectroscopy when they produce multiple origins. As we will show below, we observe two origins in our spectra, which we can associate with the syn and the anti orientations of the base relative to the ribose moiety. We have published details of our setup for laser desorption jet cooling REMPI spectrometry elsewhere.10 Sample preparation consisted of depositing neat material in powder form on graphite substrates. We moved the substrate slowly while acquiring spectra, gradually exposing fresh material. For desorption we used pulses from a Nd:YAG laser at 1064 nm with fluences on the order of 1 mJ/cm2. Desorbed neutral molecules were entrained in a supersonic expansion with Ar drive gas, injected by a pulsed solenoid valve. Downstream, the entrained molecules were onecolor two-photon photoionized, and the ions were detected in a reflectron time-of-flight mass spectrometer. The first photon resonantly excites the molecule, while a second photon from the same laser ionizes the excited molecule. By varying the wavelength while monitoring specific mass peaks we obtained mass selected excitation spectra. The typical ionization laser fluence was on the order of 0.1 mJ/cm2. Figure 1 shows the REMPI spectra of (a) Gs, (b) 3′deoxyGs, and (c) 2′deoxyGs. We assign the lowest-energy peak in each of the spectra as a 0-0 transition to the S1 excited state. Careful scans to lower energy by 1000 cm-1 do not reveal any additional peaks. The same was true when performing two-color ionization with a second photon at 193 nm. Therefore, we do not believe that we are observing a cutoff in the spectrum related to the ionization potential of Gs. Furthermore we have measured the ionization potential of guanine as 8.1 eV by two-color ionization.11,12 That is 1 eV less than the two-photon energy at the Gs origin. † Heinrich Heine Universität. (1) Nir, E.; Grace, L.; Brauer, B.; de Vries, M. S. J. Am. Chem. Soc. 1999, 121, 4896. (2) Faurskov-Nielsen, O.; Lund, P.; Petersen, S. J. Raman Spectrosc. 1981, 11, 493. (3) Nishimura, Y.; Tsuboi, M.; Sato, T.; Aoki, K. J. Mol. Struct. 1986, 146, 123. (4) Chinsky, L.; Jolles, B.; Laigle, A.; Turpin, P. J. Raman Spectrosc. 1987, 18, 195. (5) Carmona, P.; Molina, M. J. Mol. Struct. 1990, 219, 323. (6) Toyama, A.; Takino, Y.; Takeuchi, H.; Harada, I. J. Am. Chem. Soc. 1993, 115, 11092. (7) Urabe, H.; Sugawara, Y.; Kasuya, T. Phys. ReV. B 1995, 51, 5666. (8) Toyama, A.; Hamuara, M.; Takeuchi, H. J. Mol. Struct. 1996, 15, 99. (9) Toyama, A.; Hanada, N.; Ono, J.; Yoshimitsu, E.; Takeuchi, H. J. Raman Spectrosc. 1999, 30, 623. (10) Meijer, G.; de Vries, M. S.; Hunziker, H. E.; Wendt, H. R. Appl. Phys. B 1990, 51, 395. (11) Hopkins, J. B.; Powers, D. R.; Smalley, R. E. J. Phys. Chem. 1981, 85, 3739. (12) Nir, E.; Grace, L.; de Vries, M. S. To be published. Figure 1. REMPI spectra of (a) guanosine, (b) 3′deoxyGs, and (c) 2′deoxyGs. In this energy range guanine itself does not exhibit any vibronic activity since its lowest energy peak is at 238 cm-1 above the origin. The syn and anti labels indicate origins of two possible conformers, and the numbers indicate vibrational modes and their combinations and overtones, for example 122 indicates one quantum of mode 1 and two quanta of mode 2; f indicates fundamental vibration. 8091 J. Am. Chem. Soc. 2000, 122, 8091-8092

Laser desorption jet-cooling spectroscopy of para-amino benzoic acid monomer, dimer, and clusters

The technique of laser desorption followed by jet cooling allows wavelength‐selective as well as mass‐selective detection of molecules, desorbed from a surface without fragmentation. Resonance enhanced multi photon ionization (REMPI) spectra of the para‐amino benzoic acid (PABA) molecule and its methyl and n‐butyl ester were obtained in this way. The origin of the S1←S0 transition in PABA was found at 34173±2 cm−1. The adiabatic ionization potential of PABA was determined as 7.998±0.001 eV. In addition, jet‐cooled REMPI spectra of the PABA dimer and its ring‐deuterated isotopes were recorded. The dimer is formed by two identical hydrogen bonds between the carboxylic acid groups. The excitation in the dimer is found to be almost completely localized in one monomer unit. Clusters of PABA molecules with molecules seeded in the beam (argon, methanol, water) were resonantly detected as well, using PABA as the chromophore.

Spectroscopy on triphenylamine and its van der Waals complexes

Both vibrationally and rotationally resolved spectra of the S, + So transition in jet-cooled triphenylamine (TPA) around 340320 nm are reported. Medium resolutton spectra (0.5-l .O cm-’ resolution) are recorded using ( 1 + 1 )-resonance enhanced multi photon iomzation (REMPI) with mass selective time-of-flight (TOF) detection in a pulsed molecular beam apparatus. The origin ofthe S,+ So transition is at 29520.7 cm-‘, higher than halfway to the iomzation potential (IP) found at 6.89 eV. A vibrational progression m the symmetric torsion mode ( 1 14 cm-‘) as well as in the symmetric C-N stretching mode (280 cm-‘) is observed m the electronic spectra. The spectrum of the most abundant isomer of the TPA-Ar (TPA-Kr ) complexes is blue-shifted by 2 11 cm- I ( 2 16 cm-’ ) with respect to the spectrum of the free TPA molecule High-resolution (the resolution mamly being determined by the natural linewidth of the transition, i.e. 36 MHz) spectra are recorded using laser Induced fluorescence (LIF) in a cw molecular beam apparatus. Individual rotational transitions are resolved and the spectrum shows unambiguously that TPA is a symmetric top molecule. The rotational constant B” m the So state of TPA is equal to B”=403.7 f0.5 MHz. Upon S,+So excitation both B and C mcrease with 7.4 2 0.1 MHz and 2.8 k 0.1 MHz, respectively. The spectrum of the blue-shifted TPA-Ar isomer is the spectrum of a symmetric top molecule as well, and therefore the Ar atom has to be located on the C3 symmetry axis, either on top of or underneath the umbrella formed by the phenyl rmgs. It appears that when Ar or Kr forms a complex with TPA, the first Ar, Kr. atom goes preferentially in a position on the C, symmetry axis of TPA, a position which causes an abnormal blueshift of the spectrum. With the first rare-gas atom located m this special position, the second rare-gas atom is forced into a “normal” position, i.e. above one of the phenyl rings, causing a normal red-shift with respect to the TPA-Ar complex.

Structural information on Y ions in C82 from EXAFS experiments

Abstract EXAFS experiments on a fullerene sample containing both YC82 and Y2C82 are reported, performed both at 10 K and at room temperature, to probe the structural environment of the yttrium atoms. The results are similar at both temperatures. The data can be fit with a model with two shells of 6 carbon atoms each, at 2.4 and 2.9 A, respectively. This result supports the hypothesis that the metal atoms are trapped inside the fullerene cage, consistent with recent calculations on possible metallofullerene structures.

Orientation dependence in the reaction of Xe* with photodissociation polarized IBr

The reaction of metastable Xe* with IBr to produce XeI* and XeBr* excimers was studied in crossed molecular beams. The IBr beam was rotationally polarized by using laser photodissociation to selectively remove most of the M state distribution. The reaction cross section was found to be largest when the Xe* approaches parallel to the plane of rotation of the IBr, and smallest when the Xe* approaches perpendicular to the plane of rotation. Reaction models for excimer formation are discussed, and it is concluded that the observed steric effect results from the anisotropy of the ionic Xe+/IBr−(2Π) potential surface, involving the first excited state of IBr−, which is the intermediate state in the formation of XeI*.

Conformational Structure of Tyrosine, Tyrosyl-Glycine, and Tyrosyl-Glycyl-Glycine by Double Resonance Spectroscopy

We investigated the variation in conformation for the amino acid tyrosine (Y), alone and in the small peptides tyrosine-glycine (YG) and tyrosine-glycine-glycine (YGG), in the gas phase by using UV-UV and IR-UV double resonance spectroscopy and density functional theory calculations. For tyrosine we found seven different conformations, for YG we found four different conformations, and for YGG we found three different conformations. As the peptides get larger, we observe fewer stable conformers, despite the increasing complexity and number of degrees of freedom. We find structural trends similar to those in phenylalanine-glycine-glycine (FGG) and tryptophan-glycine-glycine (WGG); however, the effect of dispersive forces in FGG for stabilizing a folded structure is replaced by that of hydrogen bonding in YGG.