Conformation-Selective Ultraviolet-Ultraviolet Hole Burning Spectra of Ubiquitin Ions in a Cryogenic Ion Trap.

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.

Cigarette smoke impairs the hematopoietic supportive property of mesenchymal stem cells via the production of reactive oxygen species and NLRP3 activation.

BACKGROUND: Mesenchymal stem cells (MSCs) play important roles in tissue homeostasis by providing a supportive microenvironmental niche for the hematopoietic system. Cigarette smoking induces systemic abnormalities, including an impeded recovery process after hematopoietic stem cell transplantation. However, the role of cigarette smoking-mediated alterations in MSC niche function have not been investigated. METHODS: In the present study, we investigated whether exposure to cigarette smoking extract (CSE) disrupts the hematopoietic niche function of MSCs, and pathways impacted. To investigate the effects on bone marrow (BM)-derived MSCs and support of hematopoietic stem and progenitor cells (HSPCs), mice were repeatedly infused with the CSE named 3R4F, and hematopoietic stem and progenitor cells (HSPCs) supporting function was determined. The impact of 3R4F on MSCs at cellular level were screened by bulk-RNA sequencing and subsequently validated through qRT-PCR. Specific inhibitors were treated to verify the ROS or NLRP3-specific effects, and the cells were then transplanted into the animal model or subjected to coculture with HSPCs. RESULTS: Both direct ex vivo and systemic in vivo MSC exposure to 3R4F resulted in impaired engraftment in a humanized mouse model. Furthermore, transcriptomic profile analysis showed significantly upregulated signaling pathways related to reactive oxygen species (ROS), inflammation, and aging in 3R4F-treated MSCs. Notably, ingenuity pathway analysis revealed the activation of NLRP3 inflammasome signaling pathway in 3R4F-treated MSCs, and pretreatment with the NLRP3 inhibitor MCC950 rescued the HSPC-supporting ability of 3R4F-treated MSCs. CONCLUSION: In conclusion, these findings indicate that exposure to CSE reduces HSPCs supportive function of MSCs by inducing robust ROS production and subsequent NLRP3 activation.

Alcoholic Solvent-Mediated Excited-State Proton Transfer Dynamics of a Novel Dihydroxynaphthalene Dye.

The excited-state proton transfer (ESPT) reaction is an important primary photochemical process because it is closely related to photophysical properties. Although ESPT research in aqueous solutions is predominant, alcoholic solvent-mediated ESPT studies are also significant in terms of photoacid-based reactions. Especially, the research for dihydroxynaphthalenes (DHNs) has been largely neglected due to the challenging data interpretation of two hydroxyl groups. A novel fluorescent dye, resveratrone, synthesized by light irradiation of resveratrol, which is famous for its antioxidant properties, can be regarded as a type of DHN, and it has distinctive optical properties, including high quantum yield, a large two-photon absorption coefficient, a large Stokes shift, and very high biocompatibility. In this study, we investigate the overall kinetics of the optical properties of resveratrone and find evidence for alcoholic solvent-mediated ESPT involvement in the radiative properties of resveratrone with a large Stokes shift. Our investigation provides an opportunity to revisit the overlooked photophysical properties of intriguing photoacid behavior and the large Stokes shift of the dihydroxynaphthalene dye.

Anisotropic circular dichroism of jet-cooled chiral molecules.

Anisotropic circular dichroism (CD) refers to the CD of oriented molecules, which varies with the direction of light propagation toward the molecules. Thus, anisotropic CD spectroscopy has been used to investigate the orientations of molecules in anisotropic media such as liquid crystals and thin films. However, it is unclear whether anisotropic CD results from isolated chromophores or their intermolecular interactions with other atoms or molecules that form anisotropically aligned structures. Herein, anisotropic CD of isolated chiral molecules was observed for the first time. The resonant two-photon ionization CD spectra of jet-cooled pseudoephedrine and styrene oxide indicated a difference between the CD values of the P/R and Q branches of the origin bands of the S0-S1 transition. This difference may have resulted from the anisotropic CD phenomena of these molecules, which are oriented via photoselection. Although jet-cooled molecules may have nearly random orientations, those excited to the P/R or Q branch become oriented because the transition probability to these branches depends on the molecular orientation relative to the direction of light propagation. These results demonstrate that the CD spectra of cold, isolated molecules, such as those in an interstellar medium, may exhibit anisotropic CD values.

Cryogenic Ion Spectroscopy of Protonated and Sodiated Methyladenine Derivatives.

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.

Ultraviolet photodissociation circular dichroism spectroscopy of protonated L-phenylalanyl-L-alanine in a cryogenic ion trap.

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.

Bacteria-Inspired Nanomedicine.

The natural world has provided a host of materials and inspiration for the field of nanomedicine. By taking design cues from naturally occurring systems, the nanoengineering of advanced biomimetic platforms has significantly accelerated over the past decade. In particular, the biomimicry of bacteria, with their motility, taxis, immunomodulation, and overall dynamic host interactions, has elicited substantial interest and opened up exciting avenues of research. More recently, advancements in genetic engineering have given way to more complex and elegant systems with tunable control characteristics. Furthermore, bacterial derivatives such as membrane ghosts, extracellular vesicles, spores, and toxins have proven advantageous for use in nanotherapeutic applications, as they preserve many of the features from the original bacteria while also offering distinct advantages. Overall, bacteria-inspired nanomedicines can be employed in a range of therapeutic settings, from payload delivery to immunotherapy, and have proven successful in combatting both cancer and infectious disease.

Genetically engineered cell membrane-coated nanoparticles for targeted delivery of dexamethasone to inflamed lungs.

As numerous diseases are associated with increased local inflammation, directing drugs to the inflamed sites can be a powerful therapeutic strategy. One of the common characteristics of inflamed endothelial cells is the up-regulation of vascular cell adhesion molecule-1 (VCAM-1). Here, the specific affinity between very late antigen-4 (VLA-4) and VCAM-1 is exploited to produce a biomimetic nanoparticle formulation capable of targeting inflammation. The plasma membrane from cells genetically modified to constitutively express VLA-4 is coated onto polymeric nanoparticle cores, and the resulting cell membrane-coated nanoparticles exhibit enhanced affinity to target cells that overexpress VCAM-1 in vitro. A model anti-inflammatory drug, dexamethasone, is encapsulated into the nanoformulation, enabling improved delivery of the payload to inflamed lungs and significant therapeutic efficacy in vivo. Overall, this work leverages the unique advantages of biological membrane coatings to engineer additional targeting specificities using naturally occurring target-ligand interactions.

Cryogenic ion spectroscopy of adenine complexes containing alkali metal cations.

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.

Anionic Activation of CO2 via (Mn-CO2)- Complex on Magic-Numbered Anionic Coinage Metal Clusters Mn- (M = Cu, Ag, Au).

Given the immense challenge of excessive accumulation of carbon dioxide (CO2) in the earth's atmosphere, an extensive search is under way to convert atmospheric CO2 to compounds of more utility. With CO2 being thermodynamically extremely stable, activation of CO2 is the first and most important step toward its chemical conversion. Building upon our earlier model for the anionic activation of CO2 with azabenzene and inspired by the work of others on metal atom-CO2 complexes, we investigated the possibility of anionic activation of CO2 on small anionic metal clusters, which would have implications for catalytic conversion of CO2 on metal surfaces with atomic-scale structural irregularities. We carried out theoretical calculations using density functional theory to examine small anionic metal clusters of Cu, Ag, and Au to check whether they form a complex with CO2, with the sign of CO2 being chemically activated. We found that a class of anionic metal clusters Mn- with 1, 2, and 6 atoms consistently produced the activated complex (Mn-CO2)- for all three metals. There exists a strong interaction between the CO2 moiety and Mn- via a partially covalent M-C bond with a full delocalization of the electronic charge, as a result of electron transfer from the HOMO of Mn- to the LUMO of CO2 as in metal-CO2 π-backbonding. We examined the interaction of frontier orbitals from the viewpoints of the orbital geometry and orbital energetics and found that the above magic numbers are consistent with both aspects.

Selective thiolation and photoswitching mechanism of Cy5 studied by time-dependent density functional theory.

Cy5 is one of the most widely used organic dyes with a photoswitching property. It can be reversibly photoconverted to the dark state through thiolation with primary thiols. Although photoswitching of Cy5 has been widely used in super-resolution nanoscopy, its thiolation mechanism remains unclear. We carried out time-dependent density functional theory calculations to investigate the excited state dynamics of Cy5 and observed its site-selective thiolation on both the ground and excited states. Scanning the excited state potential energy surfaces by rotating individual C-C bonds revealed structural similarity between the twisted form of Cy5 and the Cy5 subunit in the thiolated Cy5, which suggests that the dark state formation is strongly associated with the torsional motion on the excited state.

Nanoparticle-hydrogel superstructures for biomedical applications.

The incorporation of nanoparticles into hydrogels yields novel superstructures that have become increasingly popular in biomedical research. Each component of these nanoparticle-hydrogel superstructures can be easily modified, resulting in platforms that are highly tunable and inherently multifunctional. The advantages of the nanoparticle and hydrogel constituents can be synergistically combined, enabling these superstructures to excel in scenarios where employing each component separately may have suboptimal outcomes. In this review, the synthesis and fabrication of different nanoparticle-hydrogel superstructures are discussed, followed by an overview of their use in a range of applications, including drug delivery, detoxification, immune modulation, and tissue engineering. Overall, these platforms hold significant clinical potential, and it is envisioned that future development along these lines will lead to unique solutions for addressing areas of pressing medical need.

Chiral and Isomeric Discrimination of Chiral Molecular Ions by Cold Ion Circular Dichroism Spectroscopy.

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.

Induced Circular Dichroism of Jet-Cooled Phenol Complexes with (R)-(-)-2-Butanol.

The induced circular dichroism (ICD) of phenol complexed with (R)-(-)-2-butanol [PhOH-(-)BOH] in a supersonic jet is investigated using resonant two-photon ionization circular dichroism (R2PICD) spectroscopy. The R2PICD spectrum of PhOH-(-)BOH exhibits nonzero ICD bands near the absorption region of bare PhOH, where (-)BOH is transparent. Two different conformers containing a single hydrogen bond between PhOH and (-)BOH are identified using ultraviolet-ultraviolet hole-burning and infrared ion-dip spectroscopy combined with quantum theoretical calculations. The ICD values of the two conformers are similar to each other. To understand these similar ICD effects of the conformers, the geometrical asymmetry of the PhOH moiety bound to (-)BOH and the coupling strength of the electric transition dipole moments between PhOH and (-)BOH are estimated. Comparing the ICD values of PhOH-(-)BOH with those of PhOH-(-)-l-methyl lactate in the previous report [ Hong , A. ; J. Phys. Chem. Lett. 2018 , 9 , 476 -480 ], we investigate the physical properties that may govern the differences of the ICD values between the two complexes.

An atomistic mechanism for the degradation of perovskite solar cells by trapped charge.

It is unmistakably paradoxical that the most vulnerable aspect of the photoactive organic-inorganic hybrid perovskite is its instability against light. Why and how perovskites break down under light irradiation and what happens at the atomistic level of these materials during the degradation process still remain unanswered. In this paper, we found the culprit and verified the mechanism for the irreversible degradation of hybrid perovskite materials from our experimental investigation and ab initio molecular dynamics (AIMD) simulation. We initially found that the electrostatic charges generated by light irradiation and trapped along the grain boundaries of the perovskite crystal result in oxygen-induced irreversible degradation in dry air. This result, together with our previous experimental finding on the same critical role of trapped charges in the perovskite degradation under moisture, suggests that the trapped charges are the main culprit in both the oxygen- and moisture-induced degradation of perovskite materials. Detailed roles of oxygen and water molecules were investigated using AIMD simulation by tracking the atomic motions in the outermost layers of the oxygen- or water-covered methylammonium lead triiodide (denoted MAPbI3 for CH3NH3PbI3) perovskite crystal with trapped charges. In the first few picoseconds of our simulation, trapped charges start disrupting the crystal structure, leading to a short-range interaction between oxygen or water molecules and the compositional ions of MAPbI3. We found that there exist different degradation pathways depending on both the polarity of the trapped charge and the kind of gas molecule. We also verified that a more structurally stable, multi-component perovskite material (with the composition of MA0.6FA0.4PbI2.9Br0.1) showed much stronger resistance against light-induced degradation than MAPbI3 even in 100%-oxygen ambience or humid air.

Isomer-Specific Induced Circular Dichroism Spectroscopy of Jet-Cooled Phenol Complexes with (-)-Methyl l-Lactate.

Induced circular dichroism (ICD) is the CD observed in the absorption of an achiral molecule bound to a transparent chiral molecule through noncovalent interactions. ICD spectroscopy has been used to probe the binding between molecules, such as protein-ligand interactions. However, most ICD spectra have been measured in solution, which only exhibit the averaged CD values of all conformational isomers in solution. Here, we obtained the first isomer-selective ICD spectra by applying resonant two-photon ionization CD spectroscopy to jet-cooled phenol complexes with (-)-methyl l-lactate (PhOH-(-)ML). The well-resolved CD bands in the spectra were assigned to two conformers, which contained different types of hydrogen-bonding interactions between PhOH and (-)ML. The ICD values of the two conformers have different signs and magnitudes, which were explained by differences both in the geometrical asymmetries of PhOH bound to (-)ML and in the electronic coupling strengths between PhOH and (-)ML.

Shedding new light on an old molecule: quinophthalone displays uncommon N-to-O excited state intramolecular proton transfer (ESIPT) between photobases.

Excited state dynamics of common yellow dye quinophthalone (QPH) was probed by femtosecond transient absorption spectroscopy. Multi-exponential decay of the excited state and significant change of rate constants upon deuterium substitution indicate that uncommon nitrogen-to-oxygen excited state intramolecular proton transfer (ESIPT) occurs. By performing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations, we found that adiabatic surface crossing between the S1 and S2 states takes place in the photoreaction. Unlike most cases of ESIPT, QPH does not exhibit tautomer emission, possibly due to internal conversion or back-proton transfer. The ESIPT of QPH presents a highly interesting case also because the moieties participating in ESIPT, quinoline and aromatic carbonyl, are both traditionally considered as photobases.

Ab initio study on anomalous structures of anionic [(N-heterocycle)-CO2]- complexes.

Several unusual anionic complexes between carbon dioxide (CO2) and N-heterocycles (NHCs) possessing a significantly positive adiabatic electron affinity over 0.7 eV were studied by density functional theory calculations (UB3LYP/6-311++g(d,p)). Unlike all previously reported [NHC-CO2]- anions with a coplanar structure that ensures full delocalization of the negative charge through extended π-conjugation, this new class of anionic [NHC-CO2]- complexes has a strongly non-coplanar geometry and no π-bond character between CO2 and NHC. Despite the fundamental differences in chemical bonding between all prior cases and the new class of [NHC-CO2]- complexes, we found that the CO2 moiety in the latter still has a large negative charge (∼0.4 e) and a strongly bent geometry (O-C-O angle of ∼140°) just like in the former. This seemingly anomalous case was explained by a simple model based on the torsional steric effect and the electron affinities of the constituent moieties.

Electronic Circular Dichroism Spectroscopy of Jet-Cooled Phenylalanine and Its Hydrated Clusters.

We obtained resonant two-photon ionization circular dichroism (R2PICD) spectra of jet-cooled phenylalanine (Phe) and its hydrated clusters (Phe(H2O)n, n = 1-2) near the origin band of the S0-S1 transition. The R2PICD spectra of Phe exhibit well-resolved CD bands of six different conformers present in the jet, which vary in sign and magnitude depending on their conformations. We revised the previous structural assignments of the Phe conformers based on the comparison between the experimental and theoretical CD signs, infrared spectra, and rotational band contours. The R2PICD spectra of Phe(H2O)n reveal that hydration with one or two water molecule(s) does not affect the CD signs of Phe conformers but significantly increases their CD magnitudes. Furthermore, conformational selection by solvation alters relative populations of Phe conformers, leading to a sign inversion in the CD spectra of Phe(H2O)n compared with that of Phe monomer.

Fluorescence-detected circular dichroism spectroscopy of jet-cooled ephedrine.

The resonant two-photon ionization circular dichroism (R2PICD) spectrum represents the cumulative circular dichroism (CD) of one-photon excitation and the subsequent one-photon ionization, whereas the fluorescence-detected circular dichroism (FDCD) spectra exhibit only the CD of one-photon excitation, similar to conventional CD spectra. We obtained the FDCD spectra of jet-cooled ephedrine (EPD) near the origin band of the S0-S1 transition to measure the CD of one-photon absorption and thus the CD of the ionization process in R2PI in comparison with the R2PICD spectra. The CD effects of the ionization following excitation of the A (0-0) and C (930 cm(-1)) bands in the spectrum are small, whereas those of the B band (530 cm(-1)) are anomalously large, leading to opposite CD signs for the FDCD and R2PICD spectra. Based on the intermediate state-selective fragmentation patterns in the R2PI spectra, this large CD effect is attributed to the state-selective isomerization that occurs after excitation of the B band. By comparing the experimental and theoretical spectra, we determined that the B band corresponds to an asymmetric ring distortion mode that involves torsional motions of the side chain, which may facilitate the isomerization process. This study demonstrates that FDCD spectroscopy combined with R2PICD spectroscopy provides a powerful tool to measure the CD effects of the excitation and ionization processes separately in R2PI and thus probe the structural changes that occur during the ionization process following excitation to an intermediate state.