Understanding the structural variations of conformational isomers in proteins is crucial for elucidating protein folding mechanisms. Here, we present a novel method for obtaining conformation-selective ultraviolet (UV)-UV hole burning (HB) spectra of ubiquitin ions ((Ubi+zH)+z, z = 7-10) produced via electrospray ionization. Our approach involves binding multiple N2 molecules to ubiquitin ions ((Ubi+zH)+z(N2)m, m = 1-55) within a cryogenic ion trap. Upon exposure to UV irradiation, efficient fragmentation of (Ubi+zH)+z(N2)m occurs, primarily yielding bare (Ubi+zH)+z ions as fragments. The significant mass difference between the parent and fragment ions facilitates the acquisition of UV-UV HB spectra, which reveal the presence of at least two distinct conformers. Molecular dynamics simulations suggest that these conformers correspond to A-state structures, differing only in the interactions of a tyrosine residue with neighboring residues. Our findings underscore UV-UV HB spectroscopy of protein ions as a powerful tool for exploring diverse protein isomers.

Ultraviolet photodissociation (UVPD) spectra of protonated 9-methyladenine (H+9MA), protonated 7-methyl adenine (H+7MA), protonated 3-methyladenine (H+3MA), and sodiated 7-methyladenine (Na+7MA) near the origin bands of the S0-S1 transition were obtained using cryogenic ion spectroscopy. The UV- UV hole burning, infrared (IR) ion-dip, and IR-UV double resonance spectra showed that all the ions were present as single isomers in a cryogenic ion trap. The UVPD spectrum of H+9MA exhibited only a broad absorption band, whereas the spectra of H+7MA, H+3MA, and Na+7MA displayed moderately or well-resolved vibronic bands. Potential energy profiles were computed to understand the reason for the different bandwidths of the vibronic bands in the spectra. The broadening of the bands was correlated with the slopes between the Franck-Condon point and the conical intersection between the S1 and S0 states in the potential energy profiles, thus reflecting the deactivation rates in the S1 state.

The nature of the electron-binding forces in the dipole-bound states (DBS) of anions is interrogated through experimental and theoretical means by investigating the autodetachment dynamics from DBS Feshbach resonances of ortho-, meta-, and para-bromophenoxide (BrPhO-). Though the charge-dipole electrostatic potential has been widely regarded to be mainly responsible for the electron binding in DBS, the effect of nonclassical electron correlation has been conceived to be quite significant in terms of its static and/or dynamic contributions toward the binding of the excess electron to the neutral core. State-specific real-time autodetachment dynamics observed by picosecond time-resolved photoelectron velocity-map imaging spectroscopy reveal that the autodetachment processes from the DBS Feshbach resonances of BrPhO- anions cannot indeed be rationalized by the conventional charge-dipole potential. Specifically, the autodetachment lifetime is drastically lengthened depending on differently positioned Br-substitution, and this rate change cannot be explained within the framework of Fermi's golden rule based on the charge-dipole assumption. High-level ab initio quantum chemical calculations with EOM-EA-CCSD, which intrinsically takes into account electron correlations, generate more reasonable predictions on the binding energies than density functional theory (DFT) calculations, and semiclassical quantum dynamics simulations based on the EOM-EA-CCSD data excellently predict the trend in the autodetachment rates. These findings illustrate that static and dynamic properties of the excess electron in the DBS are strongly influenced by correlation interactions among electrons in the nonvalence orbital of the dipole-bound electron and highly polarizable valence orbitals of the bromine atom, which, in turn, dictate the interesting chemical fate of exotic anion species.

Nonvalence bound states (NBS) are anionic states where the excess electron is extremely loosely bound to the neutral core through long-range potentials. In contrast to the valence orbitals of which the electron occupancy determines the molecular structure, as well as the chemical reactivity, the nonvalence orbital is quite diffuse and located far from the neutral core. The NBS can be classified into the dipole-bound state (DBS), quadruple-bound state (QBS), or correlation-bound state (CBS) according to the nature of the electron-neutral interaction, although their interaction potentials may cooperatively contribute. The NBS is ubiquitous in nature and has the strong implications in atmospheric, interstellar, or biological chemistry. Accordingly, NBS has long been conceived to play the role of the doorway into the formation of a stable anion or dissociative electron attachment (DEA). Despite intensive and extensive studies, however, the quantum-mechanical nature of NBS is still far from being thorough understanding. Herein, we describe a new aspect of state-specific NBS-mediated chemical dynamics, which has been revealed through a series of recent studies by our group. We have employed picosecond time-resolved pump-probe spectroscopy combined with cryogenically cooled ion trap and velocity-map imaging techniques to study closed-shell anions generated by electrospray ionization. DBS vibrational Feshbach resonances are prepared by the optical excitation of phenoxide, for instance, and their individual lifetimes have been precisely measured in a state-specific manner to reveal the strong mode-dependency of the autodetachment rate. Fermi's golden rule turns out to be extremely useful for a rational explanation of the experiment, although the more sophisticated theoretical model is desirable for the more quantitative analysis. For the DBS of para-chlorophenoxide or para-bromophenoxide where the polarizability of neutral core is substantial, the Fermi's golden rule based on the charge-dipole potential needs to be significantly modified to include the correlation effects to explain the exceptionally slow autodetachment rates. For the QBS of 4-cyanophenoxide, the mode-specific behavior of the quadrupole ellipsoid tensor explains the strong mode-dependent autodetachment rate. Meanwhile, the nonadiabatic transition of the excess electron into the valence orbital can result in stable anion formation or immediate chemical bond rupture. In the DBS of ortho-, meta-, or para-iodophenoxide, the transformation of the loosely bound excess electron into the πσ* antibonding orbital occurs to give I- as a final fragment. The fragmentation mediated by DBS occurs competitively with the concomitant autodetachment, paving a new way of the reaction control by tuning the quantum-mechanical nature of the DBS Feshbach resonance. This experimental observation provides the foremost evidence for the dynamic role of the DBS as a doorway into anion chemistry, such as DEA. The ponderomotive force on the electron in the nonvalence orbital has been demonstrated for the first time in a strong optical field, giving great promise for the manipulation of polyatomic molecules in terms of the spatial location, as well as the AC-Stark control of the chemical reaction.

Anion chemical dynamics of autodetachment and fragmentation mediated by the dipole-bound state (DBS) have been thoroughly investigated in a state-specific way by employing the picosecond time-resolved or the nanosecond frequency-resolved spectroscopy combined with the cryogenically cooled ion trap and velocity-map imaging techniques. For the ortho-, meta-, or para-iodophenoxide anion (o-, m-, or p-IPhO-), the C-I bond rupture occurs via the nonadiabatic transition from the DBS to the nearby valence-bound states (VBS) of the anion where the vibronic coupling into the S1 (πσ*) state (repulsive along the C-I bond extension coordinate) should be largely responsible. Dynamic details are governed by the isomer-specific nature of the potential energy surfaces in the vicinity of the DBS-VBS curve crossings, as manifested in the huge different chemical reactivity of o-, m-, or p-IPhO-. It is confirmed here that the C-I bond dissociation is mediated by DBS resonances, providing the foremost evidence that the metastable DBS plays the critical role as the doorway into the anion chemistry especially of the dissociative electron attachment (DEA). The fragmentation channel is dominant when it is mediated by the DBS resonances located below the electron-affinity (EA) threshold, whereas it is kinetically adjusted by the competitive autodetachment when the DBS resonances above EA convey the electron to the valence orbitals. The product yield of the C-I bond cleavage is strongly mode-dependent as the rate of the concomitant autodetachment is much influenced by the characteristics of the individual vibrational modes, paving a new way of the reaction control of the anion chemistry.

Circular dichroism (CD) spectroscopy of jet-cooled molecules provides conformation-specific CD spectra. However, its widespread utilization has been limited by the weak CD effects and the low density of gas-phase molecules. Here, we developed a dualbeam method to improve the sensitivity and accuracy of gas-phase CD measurements. Circularly and linearly polarized pulses were generated from a single laser pulse and used to irradiate a single molecular-beam pulse to produce two ion peaks. The ion peaks induced by linearly polarized pulses were subtracted from those induced by circularly polarized pulses to correct the CD values for the pulse-to-pulse fluctuations in laser power and gas density. The resonant two-photon ionization CD spectrum of (1R,2R)(-)-pseudoephedrine revealed that the standard deviations of CD values measured using the dual-beam method were three times lower than those measured using a single-beam method. The dual-beam method provides an effective, accurate, and easy-touse tool to obtain gas-phase CD spectra.

We obtained ultraviolet photodissociation (UVPD) circular dichroism (CD) spectra of protonated L-phenylalanyl-L-alanine (L-H+PheAla) near the origin band of the S0-S1 transition using cryogenic ion spectroscopy. Infrared (IR) ion-dip, IR-UV hole burning (HB) and UV-UV HB spectra showed that L-H+PheAla existed as two different conformers in a cryogenic ion trap, and they had nearly identical peptide backbones but different conformations in the Phe side chain. The UVPD CD spectra revealed that the two conformers had opposite CD signs and significantly different CD magnitudes from each other. These results demonstrate that the CD value of L-H+PheAla near the origin band is strongly influenced by the conformation of the Phe side chain.

Cryogenic ion spectroscopy was used to characterize adenine complexes containing alkali metal cations (M+A, M = Cs, Rb, K, Na, and Li) produced by electrospray ionization. The ultraviolet (UV) photodissociation spectra of the complexes stored in a cryogenic ion trap exhibited well-resolved vibronic bands near their origin bands of the S0-S1 transition. The UV-UV hole-burning and infrared ion-dip spectra showed that all the M+A ions in the ion trap were single isomers of M+A7a, where the M+ ion was not bound to canonical 9H-adenine (A9) but bound to a rare tautomer, 7H-adenine (A7). Density functional theory calculations showed lower tautomerization barriers for M+A9 than for bare A9 in aqueous solution. We suggest that M+ ions not only play a catalytic role in the tautomerization of A9 to A7 but also increase the tautomerization yield by forming stable M+A7a isomers.

Circular dichroism (CD) spectra contain information about absolute configurations and conformations of chiral compounds. However, extracting this information from CD spectra in solution is challenging, because the spectra exhibit only the averaged CD values of all different conformers. CD spectroscopy of jet-cooled molecules can provide conformation-specific CD spectra, but its application to biomolecules has been limited due to the difficulty of their production in the gas phase. Here, we obtained the first CD spectra of chiral molecular ions produced by electrospray ionization (ESI) using cold ion CD spectroscopy. Protonated l- or d-phenylalanine ions produced by ESI were stored in a cold quadrupole ion trap and irradiated by multiple laser pulses with left or right circular polarization. The CD spectra exhibited well-resolved CD bands of two conformers, whose signs were opposite to each other. This study will broaden the scope of conformation-resolved CD spectroscopy to large molecular ions without size limitations.

We obtain the ultraviolet photodissociation spectrum of adenine complexes with K+ ion stored in a cold ion trap. The spectrum near the origin band of the S0–S1 transition exhibits well-resolved vibronic bands, all of which are assigned from a single isomer by UV–UV hole-burning (HB) spectroscopy. Comparing the spectrum with theoretical spectra, we determine the structure of the isomer, where K+ is bound not to 9H-adenine (A9) but to 7H-adenine (A7). We suggest that K+A7 ions are formed in solution through tautomerization, for which the energy barrier varies greatly depending on the binding site of the K+ ion on A9.

The CD spectroscopy of a chiral compound in solution yields an average CD value derived from all of the conformations of a chiral molecule. By contrast, CD spectroscopy of cold chiral molecules in the gas phase distinguishes specific conformers of a chiral molecule, but the weak CD effect has limited the practical application of this technique. Reported herein is the first resonant two-photon ionization CD spectra of ephedrines in a supersonic jet using circularly polarized laser pulses, which were generated by synchronizing the oscillation of the photoelastic modulator with the laser firing. The spectra exhibited well-resolved CD bands which were specific for the conformations and vibrational modes of each enantiomer. The CD signs and magnitudes of the jet-cooled chiral molecules were very sensitive to their conformations and thus offered crucial information for determining the three-dimensional structures of chiral species, as conducted in combination with quantum chemical calculations.