Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters.

Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e.

Velocity map imaging with no spherical aberrations.

Velocity map imaging (VMI) is a powerful technique to deduce the kinetic energy of ions or electrons that are produced from a large volume in space with good resolution. The size of the acceptance volume is determined by the spherical aberrations of the ion optical system. Here we present an analytical derivation for velocity map imaging with no spherical aberrations.

Cascade Infrared Thermal Photon Emission.

The later stages of cooling of molecules and clusters in the interstellar medium are dominated by emission of vibrational infrared radiation. With the development of cryogenic storage it has become possible to experimentally study these processes. Recent storage ring results demonstrate that intramolecular vibrational redistribution takes place within the cooling process, and an harmonic cascade model has been used to interpret the data.

Peptide Bond Formation in the Protonated Serine Dimer Following Vacuum UV Photon-Induced Excitation.

Possible routes for intra-cluster bond formation (ICBF) in protonated serine dimers have been studied. We found no evidence of ICBF following low energy collision-induced dissociation (in correspondence with previous works), however, we do observe clear evidence for ICBF following photon absorption in the 4.6-14 eV range.

Gas Phase Bond Formation in Dipeptide Clusters.

Protein bonds between amino acids are one of the most important biological linkages that create life. The detection of amino acids in the interstellar environments and in meteorites may lead to the suggestion that amino acids came from outer space and that peptides bonds may have been created in the gas phase. Here we show experimentally the creation of covalent bonds, most likely peptide bonds, between serine dipeptides in the gas phase.

Harmonic height distribution in pickup spectroscopy within electrostatic ion beam traps.

Pickup spectroscopy is a means of determining the abundance, mass, charge, and lifetime of ions oscillating in electrostatic ion beam traps. Here, we present a framework for describing the harmonic height distribution of the Fourier transform of the pickup signal and discuss the importance of the pickup positioning, bunch dynamics, and pickup width on the harmonic height distribution. We demonstrate the methodology using measurements from a newly constructed electrostatic ion beam trap.

Clusters of betaine with positive and negative ions: Evidence for the betaine tetramer being magic.

Betaine (Bet) is a pure zwitterion with an extraordinarily large dipole moment, which allows it to form stable clusters in the gas phase of the form XBet, where X is a positive or negative ion. We show here that such clusters have a prominent magic number at N = 4 for all X ions used in this work. Nevertheless, we observe a marked difference in the fragmentation pattern of anionic and cationic clusters: while cationic clusters fragment by evaporating one betaine monomer at a time, fragmentation of anionic clusters is through fission resulting in the emission of one or several betaine molecules.

Action and Ion Mobility Spectroscopy of a Shortened Retinal Derivative.

The development of tandem ion mobility spectroscopy (IMS) known as IMS-IMS has led to extensive research into isomerizations of isolated molecules. Many recent works have focused on the retinal chromophore which is the optical switch used in animal vision. Here, we study a shortened derivative of the chromophore, which exhibits a rich IM spectrum allowing for a detailed analysis of its isomerization pathways, and show that the longer the chromophore is, the lower the barrier energies for isomerization are.

Melting proteins confined in nanodroplets with 10.6 μm light provides clues about early steps of denaturation.

Ubiquitin confined within nanodroplets was irradiated with a variable-power CO2 laser. Mass spectrometry analysis shows evidence for a protein "melting"-like transition within droplets prior to solvent evaporation and ion formation. Ion mobility spectrometry reveals that structures associated with early steps of denaturation are trapped because of short droplet lifetimes.

On the Exciton Coupling between Two Chlorophyll Pigments in the Absence of a Protein Environment: Intrinsic Effects Revealed by Theory and Experiment.

Exciton coupling between two or more chlorophyll (Chl) pigments is a key mechanism associated with the color tuning of photosynthetic proteins but it is difficult to disentangle this effect from shifts that are due to the protein microenvironment. Herein, we report the formation of the simplest coupled system, the Chl a dimer, tagged with a quaternary ammonium ion by electrospray ionization. Based on action spectroscopic studies in vacuo, the dimer complexes were found to absorb 50-70 meV to the red of the monomers under the same conditions.

Isotope Labeling Study of Retinal Chromophore Fragmentation.

Previous studies have shown that the gas-phase fragmentation of the retinal chromophore after S0-S1 photoexcitation results in a prominent fragment of mass 248 which cannot be explained by the cleavage of any single bond along the polyene chain. It was therefore theorized that the fragmentation mechanism involves a series of isomerizations and cyclization processes, and two mechanisms for these processes were suggested. Here we used isotope labeling MS-MS to provide conclusive support for the fragmentation mechanism suggested by Coughlan et al.

The Soret absorption band of isolated chlorophyll a and b tagged with quaternary ammonium ions.

We have performed gas-phase absorption spectroscopy in the Soret-band region of chlorophyll (Chl) a and b tagged by quaternary ammonium ions together with time-dependent density functional theory (TD-DFT) calculations. This band is the strongest in the visible region of metalloporphyrins and an important reporter on the microenvironment. The cationic charge tags were tetramethylammonium, tetrabutylammonium, and acetylcholine, and the dominant dissociation channel in all cases was breakage of the complex to give neutral Chl and the charge tag as determined by photoinduced dissociation mass spectroscopy.

Direct measurement of the isomerization barrier of the isolated retinal chromophore.

Isomerizations of the retinal chromophore were investigated using the IMS-IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activation voltages for isomerization for each of the reaction pathways, and by measuring the threshold activation voltage for fragmentation, the relative energies of the isomers as well as the energy barriers for isomerization were determined.

Unraveling the intrinsic color of chlorophyll.

The exact color of light absorbed by chlorophyll (Chl) pigments, the light-harvesters in photosynthesis, is tuned by the protein microenvironment, but without knowledge of the intrinsic color of Chl it remains unclear how large this effect is. Experimental first absorption energies of Chl a and b isolated in vacuo and tagged with quaternary ammonium cations are reported. The energies are largely insensitive to details of the tag structure, a finding supported by first-principles calculations using time-dependent density functional theory.

UV excited-state photoresponse of biochromophore negative ions.

Members of the green fluorescent protein (GFP) family may undergo irreversible phototransformation upon irradiation with UV light. This provides clear evidence for the importance of the higher-energy photophysics of the chromophore, which remains essentially unexplored. By using time-resolved action and photoelectron spectroscopy together with high-level electronic structure theory, we directly probe and identify higher electronically excited singlet states of the isolated para- and meta-chromophore anions of GFP.

Lifetime measurements in an electrostatic ion beam trap using image charge monitoring.

A technique for mass-selective lifetime measurements of keV ions in a linear electrostatic ion beam trap is presented. The technique is based on bunching the ions using a weak RF potential and non-destructive ion detection by a pick-up electrode. This method has no mass-limitation, possesses the advantage of inherent mass-selectivity, and offers a possibility of measuring simultaneously the lifetimes of different ion species with no need for prior mass-selection.