Characterizing the Behavior of Water Interacting with a Nano-Pore Material: A Structural Investigation in Native Environment Using Magnetic Resonance Approaches.

The study of fluid absorption, particularly that of water, into nanoporous materials has garnered increasing attention in the last decades across a broad range of disciplines. However, most investigation approaches to probe such behaviors are limited by characterization conditions and may lead to misinterpretations. In this study, a combined MRI and MAS NMR method was used to study a nanoporous silica glass to acquire information about its structural framework and interactions with confined water in a native humid environment. Specifically, MRI was used for a quantitative analysis of water extent. While MAS NMR techniques provided structural information of silicate materials, including interactive surface area and framework packing. Analysis of water spin-spin relaxation times (T2) suggested differences in water confinement within the characterized framework. Subsequent unsuccessful delivery of paramagnetic molecule into the pores enabled a quantitative assessment of the dimensions that "bottleneck" the pores. Finally, pore sizes were derived from the paramagnetic molecular size, density function theory (DFT) simulation and characterizations on standard samples. Our result matches with Brunauer-Emmett-Teller (BET) analysis that the pore size is less than 1.3 nm. The use of a paramagnetic probe for pore size determination introduces a new approach of characterization in the liquid phase, offering an alternative to the conventional BET analysis that uses gas molecule as probes.

Revisiting ultrasmall phosphine-stabilized rhodium-doped gold clusters AunRh (n = 5, 6, 7, 8): geometric, electronic, and vibrational properties.

Incorporation of other transition metals in Au nanoclusters has been thriving recently due to its effect on their electronic and photophysical properties. Here, the ultrasmall phosphine-stabilized Rh-doped gold clusters AunRh (n = 5, 6, 7, 8), with metal core structures represented as fragments of a rhodium-centered icosahedron, are considered. The geometric and electronic properties of these nanoclusters are revisited and analyzed using density functional theory (DFT). Moreover, infrared spectra are simulated to identify the effects of Rh doping on the clusters through vibrational properties. Peaks are assigned to breathing-like normal modes for all AuRh clusters except for Au8Rh, likely due to the presence of bound Cl ligands. Unlike their pure gold core counterparts, the % motions of both Au and Rh atoms are lower in the mixed metal clusters, suggesting more restrained metal cores by rhodium, which could result in other novel physical and chemical properties not hitherto discovered.

An efficient and universal parallel algorithm for high-dimensional quantum dynamics in poly-atomic reactions.

This study presents a parallel algorithm for high-dimensional quantum dynamics simulations in poly atomic reactions, integrating distributed- and shared-memory models. The distributions of the wave function and potential energy matrix across message passing interface processes are based on bundled radial and angular dimensions, with implementations featuring either two- or one-sided communication schemes. Using realistic parameters for the H + NH3 reaction, performance assessment reveals linear scalability, exceeding 90% efficiency with up to 600 processors. In addition, owing to the universal and concise structure, the algorithm demonstrates remarkable extensibility to diverse reaction systems, as demonstrated by successes with six-atom and four-atom reactions. This work establishes a robust foundation for high-dimensional dynamics studies, showcasing the algorithm's efficiency, scalability, and adaptability. The algorithm's potential as a valuable tool for unraveling quantum dynamics complexities is underscored, paving the way for future advancements in the field.

Evaluating the Use of Graph Neural Networks and Transfer Learning for Oral Bioavailability Prediction.

Oral bioavailability is a pharmacokinetic property that plays an important role in drug discovery. Recently developed computational models involve the use of molecular descriptors, fingerprints, and conventional machine-learning models. However, determining the type of molecular descriptors requires domain expert knowledge and time for feature selection. With the emergence of the graph neural network (GNN), models can be trained to automatically extract features that they deem important. In this article, we exploited the automatic feature selection of GNN to predict oral bioavailability. To enhance the prediction performance of GNN, we utilized transfer learning by pre-training a model to predict solubility and obtained a final average accuracy of 0.797, an F1 score of 0.840, and an AUC-ROC of 0.867, which outperformed previous studies on predicting oral bioavailability with the same test data set.

Regulating polystyrene glass transition temperature by varying the hydration levels of aromatic ring/Li+ interaction.

Polymer properties can be altered via lithium ion doping, whereby adsorbed Li+ binds with H2O within the polymer chain. However, direct spectroscopic evidence of the tightness of Li+/H2O binding in the solid state is limited, and the impact of Li+ on polymer sidechain packing is rarely reported. Here, we investigate a polystyrene/H2O/LiCl system using solid-state NMR, from which we determined a dipolar coupling of 11.4 kHz between adsorbed Li+ and H2O protons. This coupling corroborates a model whereby Li+ interacts with the oxygen atom in H2O via charge affinity, which we believe is the main driving force of Li+ binding. We demonstrated the impact of hydrated Li+ on sidechain packing and dynamics in polystyrene using proton-detected solid-state NMR. Experimental data and density functional theory (DFT) simulations revealed that the addition of Li+ and the increase in the hydration levels of Li+, coupled with aromatic ring binding, change the energy barrier of sidechain packing and dynamics and, consequently, changes the glass transition temperature of polystyrene.

Catalytic Approach toward Chiral P,N-Chelate Complexes Utilizing the Asymmetric Hydrophosphination Protocol.

A synthetic procedure for obtaining a chiral P,N ligand was developed by exploiting the versatility of the asymmetric hydrophosphination protocol catalyzed by a phosphapalladacycle complex. The addition of the synthesized ligand to various metal sources led to the generation of chiral and enantioenriched chelate complexes, which can be useful prototypes for catalyst design in the future. The resulting coordination compounds were comprehensively characterized by solid-state (X-ray crystallography) and solution-based (one- and two-dimensional NMR spectroscopy) techniques and natural bond orbital (density functional theory) analysis to determine their structural and key electronic features.

Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A-U pairs in dsRNAs.

Double-stranded RNA (dsRNA) structures form triplexes and RNA-protein complexes through binding to single-stranded RNA (ssRNA) regions and proteins, respectively, for diverse biological functions. Hence, targeting dsRNAs through major-groove triplex formation is a promising strategy for the development of chemical probes and potential therapeutics. Short (e.g., 6-10 mer) chemically-modified Peptide Nucleic Acids (PNAs) have been developed that bind to dsRNAs sequence specifically at physiological conditions. For example, a PNA incorporating a modified base thio-pseudoisocytosine (L) has an enhanced recognition of a G-C pair in an RNA duplex through major-groove L·G-C base triple formation at physiological pH, with reduced pH dependence as observed for C+·G-C base triple formation. Currently, an unmodified T base is often incorporated into PNAs to recognize a Watson-Crick A-U pair through major-groove T·A-U base triple formation. A substitution of the 5-methyl group in T by hydrogen and halogen atoms (F, Cl, Br, and I) causes a decrease of the pKa of N3 nitrogen atom, which may result in improved hydrogen bonding in addition to enhanced base stacking interactions. Here, we synthesized a series of PNAs incorporating uracil and halouracils, followed by binding studies by non-denaturing polyacrylamide gel electrophoresis, circular dichroism, and thermal melting. Our results suggest that replacing T with uracil and halouracils may enhance the recognition of an A-U pair by PNA·RNA2 triplex formation in a sequence-dependent manner, underscoring the importance of local stacking interactions. Incorporating bromouracils and chlorouracils into a PNA results in a significantly reduced pH dependence of triplex formation even for PNAs containing C bases, likely due to an upshift of the apparent pKa of N3 atoms of C bases. Thus, halogenation and other chemical modifications may be utilized to enhance hydrogen bonding of the adjacent base triples and thus triplex formation. Furthermore, our experimental and computational modelling data suggest that PNA·RNA2 triplexes may be stabilized by incorporating a BrUL step but not an LBrU step, in dsRNA-binding PNAs.

General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase.

Chemically modified peptide nucleic acids (PNAs) show great promise in the recognition of RNA duplexes by major-groove PNA·RNA-RNA triplex formation. Triplex formation is favored for RNA duplexes with a purine tract within one of the RNA duplex strands, and is severely destabilized if the purine tract is interrupted by pyrimidine residues. Here, we report the synthesis of a PNA monomer incorporated with an artificial nucleobase S, followed by the binding studies of a series of S-modified PNAs. Our data suggest that an S residue incorporated into short 8-mer dsRNA-binding PNAs (dbPNAs) can recognize internal Watson-Crick C-G and U-A, and wobble U-G base pairs (but not G-C, A-U, and G-U pairs) in RNA duplexes. The short S-modified PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. Interestingly, replacement of the C residue in an S·C-G triple with a 5-methyl C results in the disruption of the triplex, probably due to a steric clash between S and 5-methyl C. Previously reported PNA E base shows recognition of U-A and A-U pairs, but not a U-G pair. Thus, S-modified dbPNAs may be uniquely useful for the general recognition of RNA U-G, U-A, and C-G pairs. Shortening the succinyl linker of our PNA S monomer by one carbon atom to have a malonyl linker causes a severe destabilization of triplex formation. Our experimental and modeling data indicate that part of the succinyl moiety in a PNA S monomer may serve to expand the S base forming stacking interactions with adjacent PNA bases.

Sequence- And Structure-Specific Probing of RNAs by Short Nucleobase-Modified dsRNA-Binding PNAs Incorporating a Fluorescent Light-up Uracil Analog.

RNAs are emerging as important biomarkers and therapeutic targets. The strategy of directly targeting double-stranded RNA (dsRNA) by triplex-formation is relatively underexplored mainly due to the weak binding at physiological conditions for the traditional triplex-forming oligonucleotides (TFOs). Compared to DNA and RNA, peptide nucleic acids (PNAs) are chemically stable and have a neutral peptide-like backbone, and thus, they show significantly enhanced binding to natural nucleic acids. We have successfully developed nucleobase-modified dsRNA-binding PNAs (dbPNAs) to facilitate structure-specific and selective recognition of dsRNA over single-stranded RNA (ssRNA) and dsDNA regions at near-physiological conditions. The triplex formation strategy facilitates the targeting of not only the sequence but also the secondary structure of RNA. Here, we report the development of novel dbPNA-based fluorescent light-up probes through the incorporation of A-U pair-recognizing 5-benzothiophene uracil (btU). The incorporation of btU into dbPNAs does not affect the binding affinity toward dsRNAs significantly, in most cases, as evidenced by our nondenaturing gel shift assay data. The blue fluorescence emission intensity of btU-modified dbPNAs is sequence- and structure-specifically enhanced by dsRNAs, including the influenza viral RNA panhandle duplex and HIV-1-1 ribosomal frameshift-inducing RNA hairpin, but not ssRNAs or DNAs, at 200 mM NaCl, pH 7.5. Thus, dbPNAs incorporating btU-modified and other further modified fluorescent nucleobases will be useful biochemical tools for probing and detecting RNA structures, interactions, and functions.

Metal-Free Fast Azidation by Using Tetrabutylammonium Azide: Effective Synthesis of Alkyl Azides and Well-Defined Azido-End Polymethacrylates.

An effective method to synthesize azido-end polymethacrylates from tetrabutylammonium azide (BNN3 ) in a nonpolar solvent (toluene) was developed. Several low-mass alkyl halides were reacted with BNN3 in toluene as model reactions and the rate constants of these reactions were determined, to confirm fast BNN3 azidation for tertiary and secondary halides. The end-group transformation of halide-end polymethacrylates was effective and nearly quantitative. Notably, the combination of organocatalyzed living (or reversible deactivation) radical polymerization and BNN3 azidation enabled the metal-free synthesis of azido-end polymethacrylates, including single-azido-end and multi-azido-end functional homopolymers and block copolymers. The rapid and quantitative reaction without the requirement for a large excess of BNN3 , metal-free and polar-solvent-free nature, and broad polymer scope are attractive features of this azidation.

Catalytic and Mechanistic Developments of the Nickel(II) Pincer Complex-Catalyzed Hydroarsination Reaction.

Synthetic challenges have significantly slowed the development of the catalytic asymmetric hydroarsination reaction despite it being a highly attractive C-As bond formation methodology. In addition, there is a poor understanding of the main reaction steps in such reactions which limit further development in the field. Herein, key intermediates of the hydroarsination reaction catalyzed by a PCP NiII -Cl pincer complex are presented upon investigating the reaction with DFT calculations, conductivity measurements, NMR spectroscopy, and catalytic screening. The novel Ni-Cl-As interaction proposed was then contrasted against known NiII -catalyzed hydrophosphination reactions to highlight dissimilarities between them even though P and As share a close group relationship. Lastly, the asymmetric hydroarsination of nitroolefins was further developed to furnish a library of chiral organoarsines in up to 99 % yield and 80 % ee under mild conditions (-20 °C to RT) between 5 to 210 mins.

Visible Light Driven Hydrogen Evolution by Molecular Nickel Catalysts with Time-Resolved Spectroscopic and DFT Insights.

Hydrogen (H2) is a clean fuel that can potentially be a future solution for the storage of intermittent renewable energy. However, current H2 production is mainly dominated by the energy intensive steam reforming reaction, which consumes a fossil fuel, methane, and emits copious amounts of carbon dioxide as one of the byproducts. To address this challenge, we report a molecular catalyst that produces H2 from aqueous solutions, is composed of affordable, earth-abundant elements such as nickel, and has been incorporated into a system driven by visible light. Under optimized conditions, we observe a turnover number of 3880, among the best for photocatalytic H2 evolution with nickel complexes from water-methanol solutions. Through nanosecond transient absorption, electron paramagnetic resonance, and UV-vis spectroscopic measurements, and supported by density functional theory calculations, we report a detailed study of this photocatalytic H2 evolution cycle. We demonstrate that a one-electron reduced, predominantly ligand-centered, reactive Ni intermediate can be accessed under visible light irradiation using triethylamine as the sacrificial electron donor and reductive quencher of the initial photosensitizer excited state. In addition, the computational calculations suggest that the second coordination sphere ether arms can enhance the catalytic activity by promoting proton relay, similar to the mechanism among [FeFe] hydrogenases in nature. Our study can form the basis for future development of H2 evolution molecular catalysts that incorporate both ligand redox noninnocence and alternative second coordination sphere effects in artificial photosynthetic systems driven by visible light.

Naphthalimide-containing conjugated polyelectrolytes with different chain configurations.

Several donor-acceptor type conjugated polyelectrolytes containing naphthalimide are developed. Different polymer chain configurations of the backbones of polymers lead to different photophysical properties. The para-substituted polymers show extended conformations with quite low quantum yields in high polarity solvents because of twisted intramolecular charge transfer features, while the meta-substituted polymers can form helices and demonstrated significantly improved quantum yields in water and methanol, as well as achieving sensitive, ultrafast and ratiometric detection of trace methylene blue in water.

Ultrafast dissociative ionization and large-amplitude vibrational wave packet dynamics of strong-field-ionized di-iodomethane.

We employ few-cycle pulses to strong-field-ionize di-iodomethane (CH2I2) and femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy to investigate the subsequent ultrafast dissociative ionization and vibrational wave packet dynamics. Probing in the spectral region of the I 4d core-level transitions, the time-resolved XUV differential absorption spectra reveal the population of several electronic states of CH2I2 + by strong-field ionization. Global analysis reveals three distinct time scales for the observed dynamics: 20 ± 2 fs, 49 ± 6 fs, and 157 ± 9 fs, ascribed to relaxation of the CH2I2 + parent ion from the Franck-Condon region, dissociation of high-lying excited states of CH2I2 + to I+ (3P2), CH2I, and I2 + (2Π3/2,g), and dissociation of CH2I2 + to I (2P3/2) and CH2I+, respectively. Oscillatory features in the time-resolved XUV differential absorption spectra point to the generation of vibrational wave packets in both the residual CH2I2 and the CH2I2 + parent ion. Analysis of the oscillation frequencies and phases reveals, in the case of neutral CH2I2, C-I symmetric stretching induced by bond softening and I-C-I bending driven by a combination of bond softening and R-selective depletion. In the case of CH2I2 +, both the fundamental and first overtone frequencies of the I-C-I bending mode are observed, indicating large-amplitude I-C-I bending motion, in good agreement with results obtained from ab initio simulations of the XUV transition energy along the I-C-I bend coordinate. These results show that femtosecond XUV absorption spectroscopy is well-suited for studying ultrafast photodissociation and vibrational wave packet dynamics.

Access to All-Carbon Spirocycles through a Carbene and Thiourea Cocatalytic Desymmetrization Cascade Reaction.

A new catalytic approach for rapid asymmetric access to spirocycles is disclosed. The reaction involves a carbene- and thiourea-cocatalyzed desymmetrization process with the simultaneous installation of a spirocyclic core. The use of a thiourea cocatalyst is critical to turn on this reaction, as no product was formed in the absence of a thiourea. Our study constitutes the first success in the carbene-catalyzed enantioselective synthesis of all-carbon spirocycles. The reaction products can be readily transformed into sophisticated multicyclic molecules and chiral ligands.

(Guanidine)copper Complex-Catalyzed Enantioselective Dynamic Kinetic Allylic Alkynylation under Biphasic Condition.

Highly enantioselective allylic alkynylation of racemic bromides under biphasic condition is furnished in this report. This approach employs functionalized terminal alkynes as pro-nucleophiles and provides 6- and 7-membered cyclic 1,4-enynes with high yields and excellent enantioselectivities (up to 96% ee) under mild conditions. Enantioretentive derivatizations highlight the synthetic utility of this transformation. Cold-spray ionization mass spectrometry (CSI-MS) and X-ray crystallography were used to identify some catalytic intermediates, which include guanidinium cuprate ion pairs and a copper-alkynide complex. A linear correlation between the enantiopurity of the catalyst and reaction product indicates the presence of a copper complex bearing a single guanidine ligand at the enantio-determining step. Further experimental and computational studies supported that the alkynylation of allylic bromide underwent an anti-SN2' pathway catalyzed by nucleophilic cuprate species. Moreover, metal-assisted racemization of allylic bromide allowed the reaction to proceed in a dynamic kinetic fashion to afford the major enantiomer in high yield.

Degenerative xanthate transfer to olefins under visible-light photocatalysis.

The degenerative transfer of xanthates to olefins is enabled by the iridium-based photocatalyst [Ir{dF(CF3)ppy}2(dtbbpy)](PF6) under blue LED light irradiation. Detailed mechanistic investigations through kinetics and photophysical studies revealed that the process operates under a radical chain mechanism, which is initiated through triplet-sensitization of xanthates by the long-lived triplet state of the iridium-based photocatalyst.

π-Conjugated Discrete Oligomers Containing Planar and Nonplanar Aromatic Motifs.

A new family of π-conjugated oligomers featuring a nonplanar polycyclic aromatic hydrocarbon, corannulene, and a planar aromatic unit, thiophene, is synthesized through an iterative metal-catalyzed coupling protocol. The two structural motifs are connected through an acetylene linkage. In the shorter oligomers, a thiophene unit is attached to one or two corannulenes. In the higher analogues, two, three, and four thiophene units are placed in an alternating fashion with three, four, and five corannulene units, respectively. Photophysical studies reveal extended π-effects that initially increase and then attenuate as a function of the oligomer length. Notably, longer oligomers are found to be highly active for nonlinear absorption and emission properties. The oligomer with three corannulene and two thiophene units exhibits a two-photon absorption cross section of 600 GM and two-photon-excited intense green luminescence. This work, therefore, introduces the concept of combining planar and nonplanar aromatic motifs in the design of π-conjugated discrete oligomers, establishes synthetic feasibility of such hybrid materials, reports on their photophysical properties that is anticipated to have significant implications for future research targets, and features the discovery that corannulene derivatives can exhibit excellent nonlinear optical activity when extended through π-bridges.

Efficient Long-Range Hole Transport Through G-Quadruplexes.

DNA offers a means of long-range charge transport for biology and electric nanodevices. Here, a series of tetra-stranded G-quadruplexes were assembled within a dendritic DNA architecture to explore oxidative charge transport (hole transport) through the G-quadruplex. Efficient charge transport was achieved over 28 Šupon UV irradiation. Over a longer G-quadruplex bridge, hole transport was escalated to a higher efficiency, which resulted in a higher yield than that of the optimal duplex DNA for charge transport, that is, the adenine tract. Efficient long-range hole transport suggests tetra-stranded G-quadruplexes, instead of an oxidation hotspot, hold better potential as an electron conduit than duplex DNA.

Investigation on Eigenfrequency of a Cylindrical Shell Resonator under Resonator-Top Trimming Methods.

The eigenfrequency of a resonator plays a significant role in the operation of a cylindrical shell vibrating gyroscope, and trimming is aimed at eliminating the frequency split that is the difference of eigenfrequency between two work modes. In this paper, the effects on eigenfrequency under resonator-top trimming methods that trim the top of the resonator wall are investigated by simulation and experiments. Simulation results show that the eigenfrequency of the trimmed mode increases in the holes-trimming method, whereas it decreases in the grooves-trimming method. At the same time, the untrimmed modes decrease in both holes-trimming and grooves-trimming methods. Moreover, grooves-trimming is more efficient than holes-trimming, which indicates that grooves-trimming can be a primary trimming method, and holes-trimming can be a precision trimming method. The rigidity condition after grooves-trimming is also studied to explain the variation of eigenfrequency. A femtosecond laser is employed in the resonator trimming experiment by the precise ablation of the material. Experimental results are in agreement with the simulation results.