Gas-Phase IR Spectroscopy of Nucleobases

Vries, Mattanjah S. de

doi:10.1007/128_2014_577

Cited by 13 publications

(22 citation statements)

References 106 publications

(92 reference statements)

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“…What distinguishes short lived, and thus UV-robust, compounds from their long lived counterparts are variations in excited state potential landscapes, resulting from structural variations. Figure 4 shows examples with three of the canonical nucleobases and hypoxanthine in the left column and some of their derivatives in the right column 5,[31][32][81][82] . When probed at energies close to the onset of absorption, all compounds in the left column have excited state lifetimes of the order of picoseconds or less, while those in the right column have lifetimes of the order of nanoseconds.…”

Section: Derivativesmentioning

confidence: 99%

How nature covers its bases

Boldissar

Vries

2018

Phys. Chem. Chem. Phys.

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The response of DNA and RNA bases to ultraviolet (UV) radiation has been receiving increasing attention for a number of important reasons: (i) the selection of the building blocks of life on an early earth may have been mediated by UV photochemistry, (ii) radiative damage of DNA depends critically on its photochemical properties, and (iii) the processes involved are quite general and play a role in more biomolecules as well as in other compounds. A growing number of groups worldwide have been studying the photochemistry of nucleobases and their derivatives. Here we focus on gas phase studies, which (i) reveal intrinsic properties distinct from effects from the molecular environment, (ii) allow for the most detailed comparison with the highest levels of computational theory, and (iii) provide isomeric selectivity. From the work so far a picture is emerging of rapid decay pathways following UV excitation. The main understanding, which is now well established, is that canonical nucleobases, when absorbing UV radiation, tend to eliminate the resulting electronic excitation by internal conversion (IC) to the electronic ground state in picoseconds or less. The availability of this rapid "safe" de-excitation pathway turns out to depend exquisitely on molecular structure. The canonical DNA and RNA bases are generally short-lived in the excited state, and thus UV protected. Many closely related compounds are longer lived, and thus more prone to other, potentially harmful, photochemical processes. It is this structure dependence that suggests a mechanism for the chemical selection of the building blocks of life on an early earth. However, the picture is far from complete and many new questions now arise.

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Section: Derivativesmentioning

confidence: 99%

How nature covers its bases

Boldissar

Vries

2018

Phys. Chem. Chem. Phys.

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“…For the experiments discussed in Chaps. [37][38][39] of this book, molecules are desorbed from a sample bar of ultrafine grain graphite with a low intensity pulsed Nd:YAG laser (fundamental or frequency doubled) with output energies of about 1-2 mJ.…”

Section: Transfer Into the Gas Phase: Laser Desorptionmentioning

confidence: 99%

IR Spectroscopic Techniques to Study Isolated Biomolecules

Rijs

2014

Topics in Current Chemistry

109

154

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The combination of mass spectrometry, infrared action spectroscopy and quantum-chemical calculations provides a variety of approaches to the study of the structure of biologically relevant molecules in vacuo. This chapter reviews some of the experimental methods that are currently in use, which can roughly be divided into two main categories: (1) low-temperature neutral molecules in a molecular beam environment, which can be investigated in a conformationally selective manner by the application of double-resonance laser spectroscopy and (2) ionized species which can conveniently be manipulated and selected by mass spectrometric methods and which can be investigated spectroscopically by wavelength-dependent photo-dissociation. Both approaches rely on the application of infrared tunable laser spectroscopy and the laser sources most commonly used in current studies are briefly reviewed in Sect. 3. Along with quantum-chemical calculations, reviewed in Chapter 3 of this book (Gaigeot and Spezia, Top Curr Chem doi:10.1007/128_2014_620), the experimental IR spectra reveal a wealth of information on the structural properties of the biological species.

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“…This approach has allowed the study of numerous flexible biological building blocks, consisting of backbones and side chains and existing as various conformers and isomers. [1][2][3][4][5][6][7][8]10 Although the energy barrier between conformers or isomers is relatively low, LDJC allows isolating specific species.…”

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“…The development of a variety of spectroscopic techniques, combined with quantum molecular calculations, has made significant contributions to the study of structural and dynamical properties of biomolecules. − These methods include ion- and fluorescence-dip spectroscopies, with tunable microwave (MW), infrared (IR), , visible (VIS), , and ultraviolet (UV) sources. In most cases, pump sources resonantly deplete the population of specific rovibrational states of ground-state molecules, subsequently probed by an additional laser beam, via action spectroscopy, involving laser-induced fluorescence and resonance-enhanced multi- or two-photon ionization (REMPI or R2PI). , This population depletion leads to reduced fluorescence or ion signals for excitations induced by the pump and probed from a shared level.…”

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“…These double-resonant or hole-burning (HB) techniques probe vibronic or vibrational transitions of specific isomers, like conformers, tautomers, or cluster structures. Implementations include UV–UV HB, infrared-ion-dip spectroscopy (IR-IDS), − and ionization-loss stimulated Raman spectroscopy (ILSRS). ,,, In IR-IDS, it is possible to obtain IR signatures by scanning the IR “burn” wavelength while monitoring the R2PI ion signal from a “probe” UV laser, tuned to the transition of a specific isomer. Since IR lasers are relatively limited in their wavelength range, most studies refer to the region covering the hydride stretch frequencies, while the assessment of far IR vibrational modes in 200–1800 cm –1 range so far has been achieved only at a free-electron laser (FEL) facility with lower resolution.…”

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Revealing the Structure and Noncovalent Interactions of Isolated Molecules by Laser-Desorption/Ionization-Loss Stimulated Raman Spectroscopy and Quantum Calculations

Shachar

Kallos

Vries

et al. 2021

J. Phys. Chem. Lett.

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The structural and dynamical characteristics of isolated molecules are essential, yet obtaining this information is difficult. We demonstrate laser-desorption jet-cooling/ionization-loss stimulated Raman spectroscopy to obtain Raman spectral signatures of nonvolatile molecules in the gas phase. The vibrational features of a test substance, the most abundant conformer of tryptamine, are compared and found to match those resulting from the scaled harmonic Raman spectrum obtained by density functional theory calculations. The vibrational signatures serve to identify the most prominent gauche conformer and evaluate its predicted electronic structure. These findings, together with noncovalent interaction (NCI) analysis, provide new insights into electron densities and reduced density gradients, assessing the hydrogen bonds (N–H···π and C–H···H–C) and interplay between attractive and repulsive NCIs affecting the structure. This approach accesses vibrational signatures of isolated nonvolatile molecules by tabletop lasers at uniform resolution and in a broad frequency range, promising great benefit to future studies.

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Gas-Phase IR Spectroscopy of Nucleobases

Cited by 13 publications

References 106 publications

How nature covers its bases

How nature covers its bases

IR Spectroscopic Techniques to Study Isolated Biomolecules

Revealing the Structure and Noncovalent Interactions of Isolated Molecules by Laser-Desorption/Ionization-Loss Stimulated Raman Spectroscopy and Quantum Calculations

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