LIAD-fs scheme for studies of ultrafast laser interactions with gas phase biomolecules

Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs

The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.

Velocity-map imaging of photoelectron circular dichroism in non-volatile molecules using a laser-based desorption source

We present an initial demonstration of a velocity-map imaging (VMI) experiment using a back-irradiation laser-based desorption source directly integrated into the electrode assembly. This has the potential to greatly expand the utility of the popular VMI approach by permitting its use with high density plumes of non-volatile molecular samples. Photoelectron circular dichroism measurements on the phenylalanine molecule using 400 nm multiphoton ionization are used to illustrate this novel method, revealing forward-backward emission asymmetries on the order of 7%.

Using photoelectron elliptical dichroism (PEELD) to determine real-time variation of enantiomeric excess

In this work, the photoionization of chiral molecules by an elliptically polarized, high repetition rate, femtosecond laser is probed. The resulting 3D photoelectron angular distribution shows a strong forward-backward asymmetry, which is highly dependent not only on the molecular structure but also on the ellipticity of the laser pulse. By continuously varying the laser ellipticity, we can observe molecular and enantiomer changes in real time at a previously unseen speed and precision. The technique allows enantiomeric excess of a pure compound to be measured with a 5% precision within 3 s, and a 10-min acquisition yields a precision of 0.4%. The isomers camphor and fenchone can be easily distinguished, unlike with conventional mass spectrometry. Preliminary results for the pharmaceutically interesting ibuprofen are also given, showing the capability of photoionization as a means of distinguishing larger molecular systems.

Dynamics of electronically excited states in the eumelanin building block 5,6-dihydroxyindole

We report the first excited state dynamics study of gas-phase 5,6-dihydroxyindole (5,6-DHI), a key building block of eumelanin pigments that are found throughout nature and serve as important photo-protective compounds. Time-resolved ion-yield measurements over the 241-296 nm ultraviolet photoexcitation region revealed non-adiabatic processes occurring on up to three distinct timescales. These reflect ultrafast (i.e. sub-picosecond) internal conversion within the excited state singlet manifold, and much longer-lived processes ranging from 10 ps to in excess of 1 ns. Our investigation paves the way for precisely targeted future studies of 5,6-DHI that exploit more differential measurement techniques. The work was facilitated by the use of soft laser-based thermal desorption to introduce 5,6-DHI samples into the gas phase. This approach, based on low-cost, readily available diode lasers, is straightforward, easily controllable and potentially applicable to a wide range of non-volatile molecular species.

Photo-dissociation of naphthalene dimer cations stored in a compact electrostatic ion storage ring

Naphthalene dimer cations [C₁₀H₈]₂ ⁺ have been produced by using an electron cyclotron resonance plasma ion source and stored in a compact electrostatic ion storage ring. We show that the radiative cooling of these cations is much slower than the isolated monomer naphthalene cations. We also report on photo-dissociation studies in the gas phase of naphthalene dimer cations at high internal energy. The dissociation energy is estimated to 0.5 eV in close agreement with previous measurements but a factor of 2 smaller than recent (density functional theory (DFT) and ab initio) theoretical studies. As uncertainties on theory as well as on the experiment cannot be as large as this difference, we conclude that this discrepancy may be due to temperature effects with possible isomerization. As an interpretation of the photo-dissociation spectrum of naphthalene dimer cations, we propose a tentative simple analytical model based on effective Morse potentials. These effective potentials are expected to "average" temperature effects that would apparently result in a smaller energy difference between the fundamental and dissociation states due to the twisting vibration modes of the naphthalene dimer cations.

Ultrafast dynamics in the DNA building blocks thymidine and thymine initiated by ionizing radiation

Ultrafast dynamics and fragmentation of thymidine and thymine after ionization by attosecond extreme ultraviolet radiation studied in the time-domain.

Detection of Neutral Species in the MALDI Plume Using Femtosecond Laser Ionization: Quantitative Analysis of MALDI-MS Signals Based on a Semiequilibrium Proton Transfer Model

We investigated neutral species in the matrix-assisted laser desorption and ionization (MALDI) plume using femtosecond laser ionization spectrometry with simultaneous measurement of the standard MALDI spectrum of the identical MALDI event induced by pulsed UV laser irradiation. The ratio of neutral species in the plume [A]_p/[M]_p (A = phenylalanine (Phe) or alanine (Ala), M = 2,5-dihydroxybenzoic acid (DHB)) was confirmed to be the same as that of the sample mixture in the range of [A]₀/[M]₀ = 4 × 10^-4-1, indicating the validity of the widely adopted approximation [A]_p/[M]_p = [A]₀/[M]₀ in the reaction quotient of the proton transfer reaction MH⁺ + A ⇄ M + AH⁺. An effective parameter representing the extent of thermal equilibrium in the thermal proton transfer model is introduced for the first time. Numerical simulation based on this semiequilibrium model successfully reproduced variations of MALDI signal intensities AH⁺ and MH⁺ with two parameters: the fraction of ionized matrix a ≤ 10^-5 and an effective temperature T = 1200 and 1100 K for Phe/DHB and Ala/DHB systems, respectively. These values show good agreement with those determined previously by different experimental approaches. The extent of thermal equilibrium was determined to be 95% and 98% for Phe/DHB and Ala/DHB systems, respectively, suggesting that the proton transfer reactions almost proceed to their thermal equilibrium.

Gas-Phase Femtosecond Particle Spectroscopy: A Bottom-Up Approach to Nucleotide Dynamics

We summarize how gas-phase ultrafast charged-particle spectroscopy has been used to provide an understanding of the photophysics of DNA building blocks. We focus on adenine and discuss how, following UV excitation, specific interactions determine the fates of its excited states. The dynamics can be probed using a systematic bottom-up approach that provides control over these interactions and that allows ever-larger complexes to be studied. Starting from a chromophore in adenine, the excited state decay mechanisms of adenine and chemically substituted or clustered adenine are considered and then extended to adenosine mono-, di-, and trinucleotides. We show that the gas-phase approach can offer exquisite insight into the dynamics observed in aqueous solution, but we also highlight stark differences. An outlook is provided that discusses some of the most promising developments in this bottom-up approach.

Laser-induced acoustic desorption of natural and functionalized biochromophores

Laser-induced acoustic desorption (LIAD) has recently been established as a tool for analytical chemistry. It is capable of launching intact, neutral, or low charged molecules into a high vacuum environment. This makes it ideally suited to mass spectrometry. LIAD can be used with fragile biomolecules and very massive compounds alike. Here, we apply LIAD time-of-flight mass spectrometry (TOF-MS) to the natural biochromophores chlorophyll, hemin, bilirubin, and biliverdin and to high mass fluoroalkyl-functionalized porphyrins. We characterize the variation in the molecular fragmentation patterns as a function of the desorption and the VUV postionization laser intensity. We find that LIAD can produce molecular beams an order of magnitude slower than matrix-assisted laser desorption (MALD), although this depends on the substrate material. Using titanium foils we observe a most probable velocity of 20 m/s for functionalized molecules with a mass m = 10 000 Da.

Proton irradiation of DNA nucleosides in the gas phase

Charge localization within nucleosides after proton irradiation is strongly influenced by the ionization energy of the base.

Ultrafast non-radiative decay of gas-phase nucleosides

De-excitation of DNA nucleosides on picosecond timescales was measured and found to be twice as fast as the equivalent nucleobases.

Resonantly Enhanced Multiphoton Ionization Spectrum of the Neutral Green Fluorescent Protein Chromophore

The photophysics of the green fluorescent protein is governed by the electronic structure of the chromophore at the heart of its β-barrel protein structure. We present the first two-color, resonance-enhanced, multiphoton ionization spectrum of the isolated neutral chromophore in vacuo with supporting electronic structure calculations. We find the absorption maximum to be 3.65 ± 0.05 eV (340 ± 5 nm), which is blue-shifted by 0.5 eV (55 nm) from the absorption maximum of the protein in its neutral form. Our results show that interactions between the chromophore and the protein have a significant influence on the electronic structure of the neutral chromophore during photoabsorption and provide a benchmark for the rational design of novel chromophores as fluorescent markers or photomanipulators.

Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond

In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.

Fragmentation of neutral amino acids and small peptides by intense, femtosecond laser pulses

High power femtosecond laser pulses have unique properties that could lead to their application as ionization or activation sources in mass spectrometry. By concentrating many photons into pulse lengths approaching the timescales associated with atomic motion, very strong electric field strengths are generated, which can efficiently ionize and fragment molecules without the need for resonant absorption. However, the complex interaction between these pulses and biomolecular species is not well understood. To address this issue, we have studied the interaction of intense, femtosecond pulses with a number of amino acids and small peptides. Unlike previous studies, we have used neutral forms of these molecular targets, which allowed us to investigate dissociation of radical cations without the spectra being complicated by the action of mobile protons. We found fragmentation was dominated by fast, radical-initiated dissociation close to the charge site generated by the initial ionization or from subsequent ultrafast migration of this charge. Fragments with lower yields, which are useful for structural determinations, were also observed and attributed to radical migration caused by hydrogen atom transfer within the molecule.

Observation of Ultrafast Charge Migration in an Amino Acid

We present the first direct measurement of ultrafast charge migration in a biomolecular building block - the amino acid phenylalanine. Using an extreme ultraviolet pulse of 1.5 fs duration to ionize molecules isolated in the gas phase, the location of the resulting hole was probed by a 6 fs visible/near-infrared pulse. By measuring the yield of a doubly charged ion as a function of the delay between the two pulses, the positive hole was observed to migrate to one end of the cation within 30 fs. This process is likely to originate from even faster coherent charge oscillations in the molecule being dephased by bond stretching which eventually localizes the final position of the charge. This demonstration offers a clear template for observing and controlling this phenomenon in the future.