Action Spectroscopy Research Articles

Structural Determination of Lysine-Linked Cisplatin Complexes via IRMPD Action Spectroscopy: NNs and NO- Binding Modes of Lysine to Platinum Coexist.

Despite its success as an anticancer drug, cisplatin suffers from resistance and produces side effects. To overcome these limitations, amino-acid-linked cisplatin analogues have been investigated. Lysine-linked cisplatin, Lysplatin, (Lys)PtCl2, exhibited outstanding reactivity toward DNA and RNA that differs from that of cisplatin. To gain insight into its differing reactivity, the structure of Lysplatin is examined here using infrared multiple photon dissociation (IRMPD) action spectroscopy. To probe the influence of the local chemical environment on structure, the deprotonated and sodium-cationized Lysplatin complexes are examined. Electronic structure calculations are performed to explore possible modes of binding of Lys to Pt, their relative stabilities, and to predict their infrared spectra. Comparisons of the measured IRMPD and predicted IR spectra elucidate the structures contributing to the experimental spectra. Coexistence of two modes of binding of Lys to Pt is found where Lys binds via the backbone and side-chain amino nitrogen atoms, NNs, or to the backbone amino and carboxylate oxygen atoms, NO-. Glycine-linked cisplatin and arginine-linked cisplatin complexes have previously been found to bind only via the NO- binding mode. Present results suggest that the NNs binding conformers may be key to the outstanding reactivity of Lysplatin toward DNA and RNA.

5-Halogenation of Uridine Suppresses Protonation-Induced Tautomerization and Enhances Glycosidic Bond Stability of Protonated Uridine: Investigations via IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Calculations.

Uridine (Urd), a canonical nucleoside of RNA, is the most commonly modified nucleoside among those that occur naturally. Uridine has also been an important target for the development of modified nucleoside analogues for pharmaceutical applications. In this work, the effects of 5-halogenation of uracil on the structures and glycosidic bond stabilities of protonated uridine nucleoside analogues are examined using tandem mass spectrometry and computational methods. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and theoretical calculations are performed to probe the structural influences of these modifications. Energy-resolved collision-induced dissociation experiments along with survival yield analyses are performed to probe glycosidic bond stability. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the conformations experimentally populated. Spectral signatures in the IR fingerprint and hydrogen-stretching regions allow the 2,4-dihydroxy protonated tautomers (T) and O4- and O2-protonated conformers to be readily differentiated. Comparisons between the measured and predicted spectra indicate that parallel to findings for uridine, both T and O4-protonated conformers of the 5-halouridine nucleoside analogues are populated, whereas O2-protonated conformers are not. Variations in yields of the spectral signatures characteristic of the T and O4-protonated conformers indicate that the extent of protonation-induced tautomerization is suppressed as the size of the halogen substituent increases. Trends in the energy-dependence of the survival yield curves find that 5-halogenation strengthens the glycosidic bond and that the enhancement in stability increases with the size of the halogen substituent.

UV photodissociation action spectra of protonated formylpyridines.

The first ππ* transition for protonated 2-, 3-, and 4-formylpyridine (FPH+) (m/z 108) is investigated by mass spectrometry coupled with photodissociation action spectroscopy at room temperature and 10K. The photoproduct ions are detected over 35000-43000cm-1, and the major product channel for 3-FPH+ and 4-FPH+ is the loss of CO forming protonated pyridine at m/z 80. For 2-FPH+, the CO loss product is present but a more abundant photoproduct arises from the loss of CH2O to form m/z 78. Plausible potential energy pathways that lead to dissociation are mapped out and comparisons are made to products arising from collision-induced dissociation. Although, in all cases, the elimination of CO is the overwhelming thermodynamically preferred pathway, the protonated 2-FPH+ results suggest that the CH2O product is kinetically driven and competitive with CO loss. In addition, for each isomer, radical photoproduct ions are detected at lower abundances. SCS-CC2/aug-cc-pVTZ Franck-Condon simulations assist with the assignment of vibrionic structure and adiabatic energies (0-0) for 2-FPH+ at 36 560cm-1, 37 430cm-1 for 3-FPH+, and 36 140cm-1 for 4-FPH+, yielding an accurate prediction, on average, within 620cm-1.

Excited-State Barrier Controls E → Z Photoisomerization in p-Hydroxycinnamate Biochromophores.

Molecules based on the deprotonated p-hydroxycinnamate moiety are widespread in nature, including serving as UV filters in the leaves of plants and as the biochromophore in photoactive yellow protein. The photophysical behavior of these chromophores is centered around a rapid E → Z photoisomerization by passage through a conical intersection seam. Here, we use photoisomerization and photodissociation action spectroscopies with deprotonated 4-hydroxybenzal acetone (pCK–) to characterize a wavelength-dependent bifurcation between electron autodetachment (spontaneous ejection of an electron from the S1 state because it is situated in the detachment continuum) and E → Z photoisomerization. While autodetachment occurs across the entire S1(ππ*) band (370–480 nm), E → Z photoisomerization occurs only over a blue portion of the band (370–430 nm). No E → Z photoisomerization is observed when the ketone functional group in pCK– is replaced with an ester or carboxylic acid. The wavelength-dependent bifurcation is consistent with potential energy surface calculations showing that a barrier separates the Franck–Condon region from the E → Z isomerizing conical intersection. The barrier height, which is substantially higher in the gas phase than in solution, depends on the functional group and governs whether E → Z photoisomerization occurs more rapidly than autodetachment.

Helium droplet infrared spectroscopy of the butyl radicals.

Butyl radicals (n-, s-, i-, and tert-butyl) are formed from the pyrolysis of stable precursors (1-pentyl nitrite, 2-methyl-1-butyl nitrite, isopentyl nitrite, and azo-tert-butane, respectively). The radicals are doped into a beam of liquid helium droplets and probed with infrared action spectroscopy from 2700 to 3125 cm-1, allowing for a low temperature measurement of the CH stretching region. The presence of anharmonic resonance polyads in the 2800-3000 cm-1 region complicates its interpretation. To facilitate spectral assignment, the anharmonic resonances are modeled with two model Hamiltonian approaches that explicitly couple CH stretch fundamentals to HCH bend overtones and combinations: a VPT2+K normal mode model based on coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] quartic force fields and a semi-empirical local mode model. Both of these computational methods provide generally good agreement with the experimental spectra.

Quantitative action spectroscopy reveals ARPE19 sensitivity to ultraviolet radiation at 350 nm and 380 nm

The role of ultraviolet radiation (UVR) exposure in the aetiology of retinal degeneration has been debated for decades with epidemiological evidence failing to find a clear consensus for or against it playing a role. A key reason for this is a lack of foundational research into the response of living retinal tissue to UVR in regard to modern ageing-specific parameters of tissue function. We therefore explored the response of cultured retinal pigmented epithelium (RPE), the loss of which heralds advanced visual decline, to specific wavelengths of UVR across the UV-B and UV-A bands found in natural sunlight. Using a bespoke in vitro UVR exposure apparatus coupled with bandpass filters we exposed the immortalised RPE cell line, ARPE-19, to 10 nm bands of UVR between 290 and 405 nm. Physical cell dynamics were assessed during exposure in cells cultured upon specialist electrode culture plates which allow for continuous, non-invasive electrostatic interrogation of key cell parameters during exposure such as monolayer coverage and tight-junction integrity. UVR exposures were also utilised to quantify wavelength-specific effects using a rapid cell viability assay and a phenotypic profiling assay which was leveraged to simultaneously quantify intracellular reactive oxygen species (ROS), nuclear morphology, mitochondrial stress, epithelial integrity and cell viability as part of a phenotypic profiling approach to quantifying the effects of UVR. Electrical impedance assessment revealed unforeseen detrimental effects of UV-A, beginning at 350 nm, alongside previously demonstrated UV-B impacts. Cell viability analysis also highlighted increased effects at 350 nm as well as 380 nm. Effects at 350 nm were further substantiated by high content image analysis which highlighted increased mitochondrial dysfunction and oxidative stress. We conclude that ARPE-19 cells exhibit a previously uncharacterised sensitivity to UV-A radiation, specifically at 350 nm and somewhat less at 380 nm. If upheld in vivo, such sensitivity will have impacts upon geoepidemiological risk scoring of macular sensitivity.

Kasha's Rule and Koopmans' Correlations for Electron Tunnelling through Repulsive Coulomb Barriers in a Polyanion.

The long-range electronic structure of polyanions is defined by the repulsive Coulomb barrier (RCB). Excited states can decay by resonant electron tunnelling through RCBs, but such decay has not been observed for electronically excited states other than the first excited state, suggesting a Kasha-type rule for resonant electron tunnelling. Using action spectroscopy, photoelectron imaging, and computational chemistry, we show that the fluorescein dianion, Fl2–, partially decays through electron tunnelling from the S2 excited state, thus demonstrating anti-Kasha behavior, and that resonant electron tunnelling adheres to Koopmans’ correlations, thus disentangling different channels.

Action-Absorption Spectroscopy at the Band Origin of the Deprotonated Green Fluorescent Protein Chromophore In Vacuo.

The application of action spectroscopy in connection with determination of the S0 to S1 band origin in the GFP anion model chromophore (deprotonated HBDI) is discussed. We specifically address the consequences of the lowest vibrational levels in S1 being located behind a potential-energy barrier that inhibits internal conversion to the S0 electronic ground state. Action spectroscopy based on consecutive absorption of two photons together with internal conversion will as a consequence reveal an apparent band origin that is significantly blue-shifted.

Gas-Phase Mechanism of O.- /Ni2+ -Mediated Methane Conversion to Formaldehyde.

The gas‐phase reaction of NiAl2O4 + with CH4 is studied by mass spectrometry in combination with vibrational action spectroscopy and density functional theory (DFT). Two product ions, NiAl2O4H+ and NiAl2O3H2 +, are identified in the mass spectra. The DFT calculations predict that the global minimum‐energy isomer of NiAl2O4 + contains Ni in the +II oxidation state and features a terminal Al−O.− oxygen radical site. They show that methane can react along two competing pathways leading to formation of either a methyl radical (CH3⋅) or formaldehyde (CH2O). Both reactions are initiated by hydrogen atom transfer from methane to the terminal O.− site, followed by either CH3⋅ loss or CH3⋅ migration to an O2− site next to the Ni2+ center. The CH3⋅ attaches as CH3 + to O2− and its unpaired electron is transferred to the Ni‐center reducing it to Ni+. The proposed mechanism is experimentally confirmed by vibrational spectroscopy of the reactant and two different product ions.

Gas‐Phase Mechanism of O .− /Ni 2+ ‐Mediated Methane Conversion to Formaldehyde

The gas-phase reaction of NiAl2O4+ with CH4 is studied by mass spectrometry in combination with vibrational action spectroscopy and density functional theory (DFT). Two product ions, NiAl2O4H+ and NiAl2O3H2+, are identified in the mass spectra. The DFT calculations predict that the global minimum-energy isomer of NiAl2O4+ contains Ni in the +II oxidation state and features a terminal Al−O.− oxygen radical site. They show that methane can react along two competing pathways leading to formation of either a methyl radical (CH3⋅) or formaldehyde (CH2O). Both reactions are initiated by hydrogen atom transfer from methane to the terminal O.− site, followed by either CH3⋅ loss or CH3⋅ migration to an O2− site next to the Ni2+ center. The CH3⋅ attaches as CH3+ to O2− and its unpaired electron is transferred to the Ni-center reducing it to Ni+. The proposed mechanism is experimentally confirmed by vibrational spectroscopy of the reactant and two different product ions.

Adatom Bonding Sites in a Nickel‐Fe3O4(001) Single‐Atom Model Catalyst and O2 Reactivity Unveiled by Surface Action Spectroscopy with Infrared Free‐Electron Laser Light

AbstractSingle‐atom (SA) catalysis presently receives much attention with its promise to decrease the cost of the active material while increasing the catalyst's performance. However, key details such as the exact location of SA species and their stability are often unclear due to a lack of atomic level information. Here, we show how vibrational spectra measured with surface action spectroscopy (SAS) and density functional theory (DFT) simulations can differentiate between different adatom binding sites and determine the location of Ni and Au single atoms on Fe3O4(001). We reveal that Ni and Au adatoms selectively bind to surface oxygen ions which are octahedrally coordinated to Fe ions. In addition, we find that the Ni adatoms can activate O2 to superoxide in contrast to the bare surface and Ni in subsurface positions. Overall, we unveil the advantages of combining SAS and DFT for improving the understanding of single‐atom catalysts.

Adatom Bonding Sites in a Nickel-Fe3 O4 (001) Single-Atom Model Catalyst and O2 Reactivity Unveiled by Surface Action Spectroscopy with Infrared Free-Electron Laser Light.

Single‐atom (SA) catalysis presently receives much attention with its promise to decrease the cost of the active material while increasing the catalyst's performance. However, key details such as the exact location of SA species and their stability are often unclear due to a lack of atomic level information. Here, we show how vibrational spectra measured with surface action spectroscopy (SAS) and density functional theory (DFT) simulations can differentiate between different adatom binding sites and determine the location of Ni and Au single atoms on Fe3O4(001). We reveal that Ni and Au adatoms selectively bind to surface oxygen ions which are octahedrally coordinated to Fe ions. In addition, we find that the Ni adatoms can activate O2 to superoxide in contrast to the bare surface and Ni in subsurface positions. Overall, we unveil the advantages of combining SAS and DFT for improving the understanding of single‐atom catalysts.

Radical Cascade Dissociation Pathways to Unusual Nucleobase Cation Radicals.

We report unusual dissociations of protonated RNA nucleosides tagged with radical initiator groups at ribose 5'-O and furnished with a 2',3'-O-isopropylidene protecting group. The ions undergo collision-induced radical cascade dissociations starting at the radical initiator that break down the dioxolane ring and trigger the formation of nucleobase cations and cation radicals. The adenine cation radical that was formed by radical cascade dissociations was identified by MS5 UV-vis photodissociation action spectroscopy to be a higher-energy N-3-H tautomer of the canonical ionized nucleobase. The guanine cation radical was formed by radical cascade dissociations as the N-7-H tautomer. In contrast to adenosine and guanosine, radical cascade dissociations of the tagged ribocytidine ion produced protonated cytosine, whereas tagged ribothymidine showed yet different dissociations resulting in predominant thymine loss. Reaction mechanisms were suggested for the cascade dissociations that were based on Born-Oppenheimer molecular dynamics and density functional theory calculations that were used to map the relevant parts of the potential energy surfaces for adenosine, guanosine, and cytidine radical ions. The reported radical cascade dissociations represent a new, nonredox approach to nucleobase and nucleoside cation radicals that has the potential of being expanded to the generation of various oligonucleotide cation radicals.

The Zeeman effect in CO+ observed with rotational action spectroscopy

We discuss newly measured rotational transitions of CO+ () in its vibrational ground state v = 0, in particular the fine-structure components of the N = 0−1 and N = 1−2 transitions. We employed a rotational action spectroscopic technique in a cryogenic ion trap for the measurements. The recorded low-temperature and high-resolution spectra of CO+ show resolved Zeeman splittings caused by the Earth's magnetic field. The highly accurate experimental transition frequencies and derived molecular constants agree with previous measurements and improve the spectroscopic parameters for this known interstellar molecular ion.

Experimental techniques and terminology in gas-phase ion spectroscopy.

This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass‐selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas‐phase action ion spectroscopy can make a large impact.

Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy

Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.

Infrared action spectroscopy of fundamental nitrilium ions: Protonated vinyl- and ethyl cyanide

Infrared action spectra of the protonated forms of two fundamental organic nitriles, vinyl cyanide, C2H3CN, and ethyl cyanide, C2H5CN, have been observed using the FELion 22-pole ion trap apparatus and the Free Electron Laser for Infrared eXperiments (FELIX) at Radboud University, Nijmegen (The Netherlands). Vibrational bands of both ions were observed in the wavenumber regime between 300 and 2500cm−1 and spectroscopically assigned based on results from anharmonic force field calculations performed here at the coupled cluster level of theory. As the action spectroscopy scheme used in the present study probes the Ne-tagged weakly bound complexes, C2H3CNH+−Ne and C2H5CNH+−Ne, corresponding quantum-chemical calculations of these systems were also performed. Significant blueshifts observed for the strong -CNH+ bending modes indicate that the neon atom is attached to the proton bound to the nitrile group in both molecular ions.

Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects.

The photophysics of green fluorescent protein (GFP) and red Kaede fluorescent protein (rKFP) are defined by the intrinsic properties of the light-absorbing chromophore and its interaction with the protein binding pocket. This work deploys photodissociation action spectroscopy to probe the absorption profiles for a series of synthetic GFP and rKFP chromophores as the bare anions and as complexes with the betaine zwitterion, which is assumed as a model for dipole microsolvation. Electronic structure calculations and energy decomposition analysis using Symmetry-Adapted Perturbation Theory are used to characterize gas-phase structures and complex cohesion forces. The calculations reveal a preponderance for coordination of betaine to the phenoxide deprotonation site predominantly through electrostatic forces. Calculations using the STEOM-DLPNO-CCSD method are able to reproduce absolute and relative vertical excitation energies for the bare anions and anion-betaine complexes. On the other hand, treatment of the betaine molecule with a point-charge model, in which the charges are computed from some common electron density population analysis schemes, show that just electrostatic and point-charge induction interactions are unable to account for the betaine-induced spectral shift. The present methodology could be applied to investigate cluster forces and optical properties in other gas-phase ion-zwitterion complexes.

Rotational Rest Frequencies and First Astronomical Search of Protonated Methylamine

We report first laboratory rest frequencies for rotational transitions of protonated methylamine, CH3NH3+, measured in a cryogenic 22-pole ion trap machine and employing an action spectroscopy scheme. For this prolate symmetric top molecule thirteen transitions between 80 and 240 GHz were detected in the ground vibrational state, covering JK = 2K − 1K up to JK = 6K − 5K with K = 0, 1, 2. Some transitions exhibit noticeable structure that is attributed to internal rotation splitting. As the CN radical and several of its hydrogenated and protonated forms up to methylamine, CH3NH2, are well known entities in the laboratory and in space, protonated methylamine, CH3NH3+, is a promising candidate for future radio astronomical detection.

Infrared spectroscopic signature of a hydroperoxyalkyl radical (•QOOH).

Infrared (IR) action spectroscopy is utilized to characterize a prototypical carbon-centered hydroperoxyalkyl radical (•QOOH) transiently formed in the oxidation of volatile organic compounds. The •QOOH radical formed in isobutane oxidation, 2-hydroperoxy-2-methylprop-1-yl, •CH2(CH3)2COOH, is generated in the laboratory by H-atom abstraction from tert-butyl hydroperoxide (TBHP). IR spectral features of jet-cooled and stabilized •QOOH radicals are observed from 2950 to 7050 cm-1 at energies that lie below and above the transition state barrier leading to OH radical and cyclic ether products. The observed •QOOH features include overtone OH and CH stretch transitions, combination bands involving OH or CH stretch and a lower frequency mode, and fundamental OH and CH stretch transitions. Most features arise from a single vibrational transition with band contours well simulated at a rotational temperature of 10 K. In each case, the OH products resulting from unimolecular decay of vibrationally activated •QOOH are detected by UV laser-induced fluorescence. Assignments of observed •QOOH IR transitions are guided by anharmonic frequencies computed using second order vibrational perturbation theory, a 2 + 1 model that focuses on the coupling of the OH stretch with two low-frequency torsions, as well as recently predicted statistical •QOOH unimolecular decay rates that include heavy-atom tunneling. Most of the observed vibrational transitions of •QOOH are readily distinguished from those of the TBHP precursor. The distinctive IR transitions of •QOOH, including the strong fundamental OH stretch, provide a general means for detection of •QOOH under controlled laboratory and real-world conditions.