Spectroscopic Evidence for Doubly Hydrogen-Bonded Cationic Dimers in the Solid, Liquid, and Gaseous Phases of Carboxyl-Functionalized Ionic Liquids.

Intermolecular interactions determine whether matter sticks together, gases condense into liquids, or liquids freeze into solids. The most prominent example is hydrogen bonding in water, responsible for the anomalous properties in the liquid phase and polymorphism in ice. The physical properties are also exceptional for ionic liquids (ILs), wherein a delicate balance of Coulomb interactions, hydrogen bonds, and dispersion interactions results in a broad liquid range and the vaporization of ILs as ion pairs. In this study, we show that strong, local, and directional hydrogen bonds govern the structures and arrangements in the solid, liquid, and gaseous phases of carboxyl-functionalized ILs. For that purpose, we explored the H-bonded motifs by X-ray diffraction and attenuated total reflection (ATR) infrared (IR) spectroscopy in the solid state, by ATR and transmission IR spectroscopy in the liquid phase, and by cryogenic ion vibrational predissociation spectroscopy (CIVPS) in the gaseous phase at low temperature. The analysis of the CO stretching bands reveals doubly hydrogen-bonded cationic dimers (c═c), resembling the archetype H-bond motif known for carboxylic acids. The like-charge doubly hydrogen-bonded ion pairs are present in the crystal structure of the IL, survive phase transition into the liquid state, and are still present in the gaseous phase even in (2,1) complexes wherein one counterion is removed and repulsive Coulomb interaction increased. The interpretation of the vibrational spectra is supported by quantum chemical methods. These observations have implications for the fundamental nature of the hydrogen bond between ions of like charge.

A Longitudinal Assessment of Resident and New Graduate Well-Being According to Length of Training: A Report From the Length of Training Pilot in Family Medicine.

Background & Objectives: No prior studies have examined how length of training may influence wellness. As part of the Length of Training Pilot (LoTP), we explored resident and new graduate well-being according to program year and length of training in 3- and 4-year family medicine residency training programs. METHODS: Two surveys captured data included in these analyses. One was a resident survey that included the Mayo Clinic physician-expanded Well-Being Index (eWBI) administered annually during the In-Training Examination (2014-2019). The second was administered to graduates 1 year after completion of training between 2016 and 2022 and included the same well-being questions. Response rates ranged between 77.7% and 96.8%. RESULTS: The eWBI summary scores for burnout were highest in postgraduate year 1 (PGY1) and did not differ statistically according to length of training (PGY1: 2.02 in 3-year [3YR] programs vs 1.93 in 4-year [4YR] programs, P=.55; postgraduate year 2 [PGY2]: 2.42 in 3YR programs vs 2.38 in 4YR programs, P=.83; postgraduate year 3 [PGY3]: 2.18 in 3YR programs vs 2.28 in 4YR programs, P=.59; and 2.34 in postgraduate year 4 [PGY4] for those in 4YR programs), though some statistical differences were noted for three items. New graduates' eWBI summary scores before the COVID-19 pandemic were 1.77 among 3YR graduates and 1.66 among 4YR graduates (P=.59). These scores were higher during COVID-19 at 1.89 for 3YR graduates and 2.02 for 4YR graduates (P=.62). Length of training was not associated with differences in well-being before or during COVID-19. CONCLUSIONS: We found no associations between length of training and physician well-being during training or among new graduates before or during COVID-19.

A wave of specific transcript and protein accumulation accompanies pollen dehydration.

In flowering plants, male gametes are immotile and carried by dry pollen grains to the female organ. Dehydrated pollen is thought to withstand abiotic stress when grains are dispersed from the anther to the pistil, after which sperm cells are delivered via pollen tube growth for fertilization and seed set. Yet, the underlying molecular changes accompanying dehydration and the impact on pollen development are poorly understood. To gain a systems perspective, we analyzed published transcriptomes and proteomes of developing Arabidopsis thaliana pollen. Waves of transcripts are evident as microspores develop to bicellular, tricellular, and mature pollen. Between the 'early'- and 'late'-pollen-expressed genes, an unrecognized cluster of transcripts accumulated, including those encoding late-embryogenesis abundant (LEA), desiccation-related protein, transporters, lipid-droplet associated proteins, pectin modifiers, cysteine-rich proteins, and mRNA-binding proteins. Results suggest dehydration onset initiates after bicellular pollen is formed. Proteins accumulating in mature pollen like ribosomal proteins, initiation factors, and chaperones are likely components of mRNA-protein condensates resembling 'stress' granules. Our analysis has revealed many new transcripts and proteins that accompany dehydration in developing pollen. Together with published functional studies, our results point to multiple processes, including i) protect developing pollen from hyperosmotic stress, ii) remodel the endomembrane system and walls; iii) maintain energy metabolism, iv) stabilize pre-synthesized mRNA and proteins in condensates of dry pollen, and v) equip pollen for compatibility determination at the stigma and for recovery at rehydration. These findings offer novel models and molecular candidates to further determine the mechanistic basis of dehydration and desiccation tolerance in plants.

Navigating the 16-dimensional Hilbert space of a high-spin donor qudit with electric and magnetic fields.

Efficient scaling and flexible control are key aspects of useful quantum computing hardware. Spins in semiconductors combine quantum information processing with electrons, holes or nuclei, control with electric or magnetic fields, and scalable coupling via exchange or dipole interaction. However, accessing large Hilbert space dimensions has remained challenging, due to the short-distance nature of the interactions. Here, we present an atom-based semiconductor platform where a 16-dimensional Hilbert space is built by the combined electron-nuclear states of a single antimony donor in silicon. We demonstrate the ability to navigate this large Hilbert space using both electric and magnetic fields, with gate fidelity exceeding 99.8% on the nuclear spin, and unveil fine details of the system Hamiltonian and its susceptibility to control and noise fields. These results establish high-spin donors as a rich platform for practical quantum information and to explore quantum foundations.

Hydrogen Tag Shifts as Vibrational Reporters for Positional Isomers of Formylphenides: Surprising Mobility of the Carbanion Center upon Collisional Decarboxylation of the Parent Benzoates.

Infrared photodissociation of weakly bound "mass tags" is widely used to determine the structures of ions by analyzing their vibrational spectra. Molecular hydrogen is a common choice for tagging in cryogenic radio-frequency ion traps. Although the H2 molecules can introduce distortions in the target species, we demonstrate an advantage of H2 tagging in the analysis of positional isomers adopted by the molecular anions derived from decarboxylation of formylbenzoates. Attachment of H2 to the carbanion centers of three such isomers yields distinct shifts in the H2 stretch, which can be used to determine the distribution of isomers in an unknown sample. Electronic structure calculations indicate that the position-dependent shifts are due to different reactivities of the carbanion sites with respect to an intracluster proton-transfer reaction with the H2 molecule. We exploit this spectroscopic method to quantify the surprisingly facile migrations of the anionic center that have been previously reported for phenide rearrangements.

Synergid cell calcium oscillations refine understanding of FERONIA/LORELEI signaling during interspecific hybridization.

KEY MESSAGE: Pollen tubes from closely related species and mutants lacking pollen tube MYB transcription factors are able to initiate FER/LRE-dependent synergid cell calcium oscillations. Reproductive isolation leads to the evolution of new species; however, the molecular mechanisms that maintain reproductive barriers between sympatric species are not well defined. In flowering plants, sperm cells are immotile and are delivered to female gametes by the pollen grain. After landing on the stigmatic surface, the pollen grain germinates a polarized extension, the pollen tube, into floral tissue. After growing via polar extension to the female gametes and shuttling its cargo of sperm cells through its cytoplasm, the pollen tube signals its arrival and identity to synergid cells that flank the egg. If signaling is successful, the pollen tube and receptive synergid cell burst, and sperm cells are released for fusion with female gametes. To better understand cell-cell recognition during reproduction and how reproductive barriers are maintained between closely related species, pollen tube-initiated synergid cell calcium ion dynamics were examined during interspecific crosses. It was observed that interspecific pollen tubes successfully trigger synergid cell calcium oscillations-a hallmark of reproductive success-but signaling fails downstream of key signaling genes and sperm are not released. This work further defines pollen tube-synergid cell signaling as a critical block to interspecific hybridization and suggests that the FERONIA/LORELEI signaling mechanism plays multiple parallel roles during pollen tube reception.

Characterization of the Oxazolone and Macrocyclic Motifs in the bn (n = 2-5) Product Ions from Collision-Induced Dissociation of Protonated Oligoglycine Peptides with Isomer-Selective, Cryogenic Vibrational Spectroscopy.

Collision-induced dissociation (CID) of small, protonated peptides leads to the formation of b-type fragment ions that can occur with several structural motifs driven by different covalent intramolecular bonding arrangements. Here, we characterize the so-called "oxazolone" and "macrocycle" bn ion structures that occur upon CID of oligoglycine peptides (Gn) ions (n = 2-6). This is determined by acquiring the vibrational band patterns of the cryogenically cooled, D2-tagged bn ions obtained using isomer-selective, two-color IR-IR photobleaching and analyzing them with predicted (DFT) harmonic spectra for the candidate structures. Both oxazolone and macrocyclic isomers are formed by b4, whereas only oxazolone species are created for b2 and b3 and the macrocycle is created for b5. As such, n = 4 corresponds to the minimum size where both Oxa and MC forms are present.

Pollen viability, longevity, and function in angiosperms: key drivers and prospects for improvement.

Pollen grains are central to sexual plant reproduction and their viability and longevity/storage are critical for plant physiology, ecology, plant breeding, and many plant product industries. Our goal is to present progress in assessing pollen viability/longevity along with recent advances in our understanding of the intrinsic and environmental factors that determine pollen performance: the capacity of the pollen grain to be stored, germinate, produce a pollen tube, and fertilize the ovule. We review current methods to measure pollen viability, with an eye toward advancing basic research and biotechnological applications. Importantly, we review recent advances in our understanding of how basic aspects of pollen/stigma development, pollen molecular composition, and intra- and intercellular signaling systems interact with the environment to determine pollen performance. Our goal is to point to key questions for future research, especially given that climate change will directly impact pollen viability/longevity. We find that the viability and longevity of pollen are highly sensitive to environmental conditions that affect complex interactions between maternal and paternal tissues and internal pollen physiological events. As pollen viability and longevity are critical factors for food security and adaptation to climate change, we highlight the need to develop further basic research for better understanding the complex molecular mechanisms that modulate pollen viability and applied research on developing new methods to maintain or improve pollen viability and longevity.

Intra-cluster Charge Migration upon Hydration of Protonated Formic Acid Revealed by Anharmonic Analysis of Cold Ion Vibrational Spectra.

The rates of many chemical reactions are accelerated when carried out in micron-sized droplets, but the molecular origin of the rate acceleration remains unclear. One example is the condensation reaction of 1,2-diaminobenzene with formic acid to yield benzimidazole. The observed rate enhancements have been rationalized by invoking enhanced acidity at the surface of methanol solvent droplets with low water content to enable protonation of formic acid to generate a cationic species (protonated formic acid or PFA) formed by attachment of a proton to the neutral acid. Because PFA is the key feature in this reaction mechanism, vibrational spectra of cryogenically cooled, microhydrated PFA·(H2O)n=1-6 were acquired to determine how the extent of charge localization depends on the degree of hydration. Analysis of these highly anharmonic spectra with path integral ab initio molecular dynamics simulations reveals the gradual displacement of the excess proton onto the water network in the microhydration regime at low temperatures with n = 3 as the tipping point for intra-cluster proton transfer.

Characterization of Oxidation Products from HOCl Uptake by Microhydrated Methionine Anions Using Cryogenic Ion Vibrational Spectroscopy.

The oxidation of the amino acid methionine (Met) by hypochlorous acid (HOCl) to yield methionine sulfoxide (MetO) has been implicated in both the interfacial chemistry of tropospheric sea spray aerosols and the destruction of pathogens in the immune system. Here, we investigate the reaction of deprotonated methionine water clusters, Met-·(H2O)n, with HOCl and characterize the resulting products using cryogenic ion vibrational spectroscopy and electronic structure calculations. Capture of the MetO- oxidation product in the gas phase requires the presence of water molecules attached to the reactant anion. Analysis of its vibrational band pattern confirms that the sulfide group of Met- has indeed been oxidized. Additionally, the vibrational spectrum of the anion corresponding to the uptake of HOCl by Met-·(H2O)n indicates that it exists as an "exit-channel" complex in which the Cl- product ion is bound to the COOH group following the formation of the S═O motif.

Connexin36 RNA Expression in the Cochlear Nucleus of the Echolocating Bat, Eptesicus fuscus.

PURPOSE: The echolocating bat is used as a model for studying the auditory nervous system because its specialized sensory capabilities arise from general mammalian auditory percepts such as pitch and sound source localization. These percepts are mediated by precise timing within neurons and networks of the lower auditory brainstem, where the gap junction protein Connexin36 (CX36) is expressed. Gap junctions and electrical synapses in the central nervous system are associated with fast transmission and synchronous patterns of firing within neuronal networks. The purpose of this study was to identify areas where CX36 was expressed in the bat cochlear nucleus to shed light on auditory brainstem networks in a hearing specialist animal model. METHODS: We investigated the distribution of CX36 RNA throughout the cochlear nucleus complex of the echolocating big brown bat, Eptesicus fuscus, using in situ hybridization. As a qualitative comparison, we visualized Gjd2 gene expression in the cochlear nucleus of transgenic CX36 reporter mice, species that hear ultrasound but do not echolocate. RESULTS: In both the bat and the mouse, CX36 is expressed in the anteroventral and in the dorsal cochlear nucleus, with more limited expression in the posteroventral cochlear nucleus. These results are generally consistent with previous work based on immunohistochemistry. CONCLUSION: Our data suggest that the anatomical substrate for CX36-mediated electrical neurotransmission is conserved in the mammalian CN across echolocating bats and non-echolocating mice.

UBE3A and transsynaptic complex NRXN1-CBLN1-GluD1 in a hypothalamic VMHvl-arcuate feedback circuit regulates aggression.

The circuit origins of aggression in autism spectrum disorder remain undefined. Here we report Tac1-expressing glutamatergic neurons in ventrolateral division of ventromedial hypothalamus (VMHvl) drive intermale aggression. Aggression is increased due to increases of Ube3a gene dosage in the VMHvl neurons when modeling autism due to maternal 15q11-13 triplication. Targeted deletion of increased Ube3a copies in VMHvl reverses the elevated aggression adult mice. VMHvl neurons form excitatory synapses onto hypothalamic arcuate nucleus AgRP/NPY neurons through a NRXN1-CBLN1-GluD1 transsynaptic complex and UBE3A impairs this synapse by decreasing Cbln1 gene expression. Exciting AgRP/NPY arcuate neurons leads to feedback inhibition of VMHvl neurons and inhibits aggression. Asymptomatic increases of UBE3A synergize with a heterozygous deficiency of presynaptic Nrxn1 or postsynaptic Grid1 (both ASD genes) to increase aggression. Targeted deletions of Grid1 in arcuate AgRP neurons impairs the VMHvl to AgRP/NPY neuron excitatory synapses while increasing aggression. Chemogenetic/optogenetic activation of arcuate AgRP/NPY neurons inhibits VMHvl neurons and represses aggression. These data reveal that multiple autism genes converge to regulate the VMHvl-arcuate AgRP/NPY glutamatergic synapse. The hypothalamic circuitry implicated by these data suggest impaired excitation of AgRP/NPY feedback inhibitory neurons may explain the increased aggression behavior found in genetic forms of autism.

Observation of Slow Eigen-Zundel Interconversion in H+(H2O)6 Clusters upon Isomer-Selective Vibrational Excitation and Buffer Gas Cooling in a Cryogenic Ion Trap.

The formation of isomers when trapping floppy cluster ions in a temperature-controlled ion trap is a generally observed phenomenon. This involves collisional quenching of the ions initially formed at high temperature by buffer gas cooling until their internal energies fall below the barriers in the potential energy surface that separate them. Here we explore the kinetics at play in the case of the two isomers adopted by the H+(H2O)6 cluster ion that differ in the proton accommodation motif. One of these is most like the Eigen cation with a tricoordinated hydronium motif (denoted E), and the other is most like the Zundel ion with the proton equally shared between two water molecules (denoted Z). After initial cooling to about 20 K in the radiofrequency (Paul) trap, the relative populations of these two spectroscopically distinct isomers are abruptly changed through isomer-selective photoexcitation of bands in the OH stretching region with a pulsed (∼6 ns) infrared laser while the ions are in the trap. We then monitor the relaxation of the vibrationally excited clusters and reformation of the two cold isomers by recording infrared photodissociation spectra with a second IR laser as a function of delay time from the initial excitation. The latter spectra are obtained after ejecting the trapped ions into a time-of-flight photofragmentation mass spectrometer, thus enabling long (∼0.1 s) delay times. Excitation of the Z isomer is observed to display long-lived vibrationally excited states that are collisionally cooled on a ms time scale, some of which quench into the E isomer. These excited E species then display spontaneous interconversion to the Z form on a ∼10 ms time scale. These qualitative observations set the stage for a series of experimental measurements that can provide quantitative benchmarks for theoretical simulations of cluster dynamics and the potential energy surfaces that underlie them.

Spectroscopic Characterization of the Divalent Metal Docking Motif to Isolated Cyanobenzoate: Direct Observation of Tridentate Binding to ortho-Cyanobenzoate and Implications for the CN Response.

Cryogenic ion vibrational spectra of D2-tagged cyanobenzoate (CBA) derivatives are obtained and analyzed to characterize the intrinsic spectroscopic responses of the -CO2- headgroup to its location on the ring in both the isolated anions and the cationic complexes with divalent metal ions, M2+ (M = Mg, Ca, Sr). The benzonitrile functionality establishes the different ring isomers (para, meta, ortho) according to the location of the carboxylate and provides an additional reporter on the molecular response to the proximal charge center. The aromatic carboxylates display shifts slightly smaller than those observed for a related aliphatic system upon metal ion complexation. Although the CBA anions display very similar band patterns for all three ring positions, upon complexation with metal ions, the ortho isomer yields dramatically different spectral responses in both the -CO2- moiety and the CN group. This behavior is traced to the emergence of a tridentate binding motif unique to the ortho isomer in which the metal ions bind to both the oxygen atoms of the carboxylate group and the N atom of the cyano group. In that configuration, the -CO2- moiety is oriented perpendicular to the phenyl ring, and the CN stretching fundamental is both strong and red-shifted relative to its behavior in the isolated neutral. The behaviors of the metal-bound ortho complexes occur in contrast to the usual blue shifts associated with "Lewis" type binding of metal ions end-on to -CN. The origins of these spectroscopic features are analyzed with the aid of electronic structure calculations, which also explore differences expected for complexation of monovalent cations to the ortho carboxylate. The resulting insights have implications for understanding the balance between electrostatic and steric interactions at metal binding sites in chemical and biological systems.

Effects of Microhydration on the Mechanisms of Hydrolysis and Cl- Substitution in Reactions of N2 O5 and Seawater.

The reaction of N2 O5 at atmospheric interfaces has recently received considerable attention due to its importance in atmospheric chemistry. N2 O5 reacts preferentially with Cl- to form ClNO2 /NO3 - (Cl- substitution), but can also react with H2 O to form 2HNO3 (hydrolysis). In this paper, we explore these competing reactions in a theoretical study of the clusters N2 O5 /Cl- /nH2 O (n=2-5), resulting in the identification of three reaction motifs. First, we uncovered an SN 2-type Cl- substitution reaction of N2 O5 that occurs very quickly due to low barriers to reaction. Second, we found a low-lying pathway to hydrolysis via a ClNO2 intermediate (two-step hydrolysis). Finally, we found a direct hydrolysis pathway where H2 O attacks N2 O5 (one-step hydrolysis). We find that Cl- substitution is the fastest reaction in every cluster. Between one-step and two-step hydrolysis, we find that one-step hydrolysis barriers are lower, making two-step hydrolysis (via ClNO2 intermediate) likely only when concentrations of Cl- are high.

Microhydration of the metastable N-protomer of 4-aminobenzoic acid by condensation at 80 K: H/D exchange without conversion to the more stable O-protomer.

4-aminobenzoic acid (4ABA) is a model scaffold for studying solvent-mediated proton transfer. Although protonation at the carboxylic group (O-protomer) is energetically favored in the gas phase, the N-protomer, where the proton remains on the amino group, can be kinetically trapped by electrospray ionization of 4ABA in an aprotic solvent such as acetonitrile. Here, we report the formation of the hydrated deuterium isotopologues of the N-protomers, RND3 +·(H2O)n=1-3, (R = C6H4COOD), which are generated by condensing water molecules onto the bare N-protomers in a liquid nitrogen cooled, radiofrequency octopole ion trap at 80 K. The product clusters are then transferred to a 20 K cryogenic ion trap where they are tagged with weakly bound D2 molecules. The structures of these clusters are determined by analysis of their vibrational patterns, obtained by resonant IR photodissociation. The resulting patterns confirm that the metastable N-protomer configuration remains intact even when warmed by the sequential condensation of water molecules. The attachment of H2O molecules onto the RND3 + head group also affords the opportunity to explore the possibility of H/D exchange between the acid scaffold and the proximal water network. The spectroscopic results establish that although the RND3 +·(H2O)n=1,2 clusters are formed without H/D exchange, the n = 3 cluster exhibits about 10% H/D exchange as evidenced by the appearance of the telltale HOD bands. The site of exchange on the acid is determined to be the acidic OH group by the emergence of the OH stretching fundamental in the -COOH motif.

Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator.

In May 2022, JCAMD published a Special Issue in honor of Gerald (Gerry) Maggiora, whose scientific leadership over many decades advanced the fields of computational chemistry and chemoinformatics for drug discovery. Along the way, he has impacted many researchers in both academia and the pharmaceutical industry. In this Epilogue, we explain the origins of the Festschrift and present a series of first-hand vignettes, in approximate chronological sequence, that together paint a picture of this remarkable man. Whether they highlight Gerry's endless curiosity about molecular life sciences or his willingness to challenge conventional wisdom or his generous support of junior colleagues and peers, these colleagues and collaborators are united in their appreciation of his positive influence. These tributes also reflect key trends and themes during the evolution of modern drug discovery, seen through the lens of people who worked with a visionary leader. Junior scientists will find an inspiring roadmap for creative collegiality and collaboration.

Structures and Chemical Rearrangements of Benzoate Derivatives Following Gas Phase Decarboxylation.

Decarboxylation of carboxylate ions in the gas phase provides a useful window into the chemistry displayed by these reactive carbanion intermediates. Here, we explore the species generated by decarboxylation of two benzoate derivatives: 2-formylbenzoate (2FBA) and 2-benzoylbenzoate (2BBA). The nascent product anions are transferred to a cryogenic ion trap where they are cooled to ∼15 K and analyzed by their pattern of vibrational bands obtained with IR photodissociation spectroscopy of weakly bound H2 molecules. The structures of the quenched species are then determined by comparison of these spectra with those predicted by electronic structure calculations for local minima on the potential energy surface. The 2-phenide carbanion generated by decarboxylation of 2FBA occurs in two isomeric forms that differ in the orientation of the formyl group, both of which yield a very large (∼110 cm-1) redshift in the stretching frequency of the H2 molecule attached to the anionic carbon center. Although calculated to be a local minimum, the analogous 2-phenide species could not be isolated upon decarboxylation of 2BBA. Rather, the anionic product adopts a ring-closed structure, indicating efficient nucleophilic attack on the pendant phenyl group by the nascent phenide. The barrier for ring closing is evaluated with electronic structure calculations.