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

Abstract

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.

Keywords: dynamics; spectroscopy; ultrafast.

Figure 1.

(a) The DNA nucleobases adenine (A), guanine (G), cytosine (C), thymine (T), (b) the nucleotide anion 2′-deoxy-guanosine 5′-monophosphate⁻ (dGMP⁻) and (c) aromatic amino acids tyrosine (Tyr), phenylalanine (Phe) and tryptophan (Trp).

Figure 2.

Schematic potential energy surfaces and major relaxation pathways in biologically relevant molecules following excitation to the 1ππ* state (light green line). One of the dominant pathways in DNA bases is (red) along ring-distortion coordinates. Evidence also exists for a pathway leading either to H-atom elimination (blue) or IC down to S₀ (purple) along X−H bonds where X=O or N. CIs mediating non-radiative pathways are circled where appropriate (adapted from [–20]).

Figure 3.

Schematic of a velocity map imaging arrangement used to perform TR-MS, TR-VMI or TR-PES experiments. V ₁ and V ₂ correspond to the voltages applied to the repeller and accelerator electrodes, respectively. For VMI, the voltage ratio V ₁:V ₂ is set to approximately 1:0.7. Further information regarding each technique is provided in §2.

Figure 4.

(a) kHz LD experimental set-up and (b) mass spectrum of guanine obtained via a kHz LD experiment. Reproduced with permission from [62].

Figure 5.

Excited-state lifetime measurements of 2,6-diaminopurine (a) 9H and (b) 7H tautomers. Reproduced with permission from [83].

Figure 6.

(a) Diagram of a typical LIAD source. Reproduced with permission from [87]. (b) LIAD signal intensity for various metal foil substrates. Reproduced with permission from [88].

Figure 7.

(a) Transient parent and fragment cation signals from LIAD study of phenylalanine and (b) transient of immonium²⁺ following ionization of the LIAD phenylalanine source. Reproduced with permission from [87].

Figure 8.

(a) Process for time-dependent ion signal in charged ring fragments. A, initial XUV ionization; B, initial fragmentation of charged parent (in this case, the unfragmented parent is followed further); C, charge migration of hole onto either amine or phenyl group; D, probe VIS/NIR pulse applied at some time Δt≥0. If the charge resides on the amine, there is no further fragmentation. If it resides on the phenyl, fragmentation is enhanced in the indicated channels. (b) Process for time-dependent ion signal of doubly charged amine. A, initial XUV ionization; B, initial fragmentation to immonium cation; C, charge migration. Hole oscillates between amine and phenyl site. As the C_α–C_β bond stretches the charge preferentially resides on the amine. D, probe VIS/NIR pulse applied at some time Δt≥0. If the charge resides on the amine, there is no further ionization, if it resides on the phenyl, the ionization occurs leaving a hole on both the amine and phenyl sites.

Figure 9.

Diagram of the ESI process. Reproduced with permission from [102].

Figure 10.

(a) Time-dependent mass channel signals in an ESI study of TrypH⁺. Reproduced with permission from [106]. (b) Time-dependent mass channel signals in an electrospray ionization study of LWH⁺. Reproduced with permission from [111].

Figure 11.

(a) Two-photon resonant photodetachment spectra of (top–bottom) dAMP⁻, dTMP⁻, dCMP⁻ and dGMP⁻, (b) time-resolved total electron yield of dGMP⁻ fit to two exponential decays yielding lifetimes of less than 50 fs (red) and approximately 700 fs (blue) and (c) time-resolved photoelectron spectrum of dGMP⁻. Reproduced with permission from [109].