Mapping the emergence of molecular vibrations mediating bond formation.

Fundamental studies of chemical reactions often consider the molecular dynamics along a reaction coordinate using a calculated or suggested potential energy surface1-5. But fully mapping such dynamics experimentally, by following all nuclear motions in a time-resolved manner-that is, the motions of wavepackets-is challenging and has not yet been realized even for the simple stereotypical bimolecular reaction6-8: A-B + C â†’ A + B-C. Here we track the trajectories of these vibrational wavepackets during photoinduced bond formation of the gold trimer complex [Au(CN)2-]3 in an aqueous monomer solution, using femtosecond X-ray liquidography9-12 with X-ray free-electron lasers13,14. In the complex, which forms when three monomers A, B and C cluster together through non-covalent interactions15,16, the distance between A and B is shorter than that between B and C. Tracking the wavepacket in three-dimensional nuclear coordinates reveals that within the first 60 femtoseconds after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 femtoseconds to give a linear and covalently bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we map and unambiguously assign to specific normal modes using only the experimental data. In principle, more intense X-rays could visualize the motion not only of highly scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door to the direct tracking of the atomic motions involved in many chemical reactions.

Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.

The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.

MicroRNAs in Dystrophinopathy.

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD), which represent the range of dystrophinopathies, account for nearly 80% of muscle dystrophy. DMD and BMD result from the loss of a functional dystrophin protein, and the leading cause of death in these patients is cardiac remodeling and heart failure. The pathogenesis and progression of the more severe form of DMD have been extensively studied and are controlled by many determinants, including microRNAs (miRNAs). The regulatory role of miRNAs in muscle function and the differential miRNA expression in muscular dystrophy indicate the clinical significance of miRNAs. This review discusses the relevant microRNAs as potential biomarkers and therapeutic targets for DMD and DMD cardiomyopathy as examples of dystrophinopathies.

Influence of Structural Defects on Biomineralized ZnS Nanoparticle Dissolution: An in-Situ Electron Microscopy Study.

The dissolution of metal sulfides, such as ZnS, is an important biogeochemical process affecting fate and transport of trace metals in the environment. However, current studies of in situ dissolution of metal sulfides and the effects of structural defects on dissolution are lacking. Here we have examined the dissolution behavior of ZnS nanoparticles synthesized via several abiotic and biological pathways. Specifically, we have examined biogenic ZnS nanoparticles produced by an anaerobic, metal-reducing bacterium Thermoanaerobacter sp. X513 in a Zn-amended, thiosulfate-containing growth medium in the presence or absence of silver (Ag), and abiogenic ZnS nanoparticles were produced by mixing an aqueous Zn solution with either H2S-rich gas or Na2S solution. The size distribution, crystal structure, aggregation behavior, and internal defects of the synthesized ZnS nanoparticles were examined using high-resolution transmission electron microscopy (TEM) coupled with X-ray energy dispersive spectroscopy. The characterization results show that both the biogenic and abiogenic samples were dominantly composed of sphalerite. In the absence of Ag, the biogenic ZnS nanoparticles were significantly larger (i.e., ∼10 nm) than the abiogenic ones (i.e., ∼3-5 nm) and contained structural defects (e.g., twins and stacking faults). The presence of trace Ag showed a restraining effect on the particle size of the biogenic ZnS, resulting in quantum-dot-sized nanoparticles (i.e., ∼3 nm). In situ dissolution experiments for the synthesized ZnS were conducted with a liquid-cell TEM (LCTEM), and the primary factors (i.e., the presence or absence structural defects) were evaluated for their effects on the dissolution behavior using the biogenic and abiogenic ZnS nanoparticle samples with the largest average particle size. Analysis of the dissolution results (i.e., change in particle radius with time) using the Kelvin equation shows that the defect-bearing biogenic ZnS nanoparticles (γ = 0.799 J/m2) have a significantly higher surface energy than the abiogenic ZnS nanoparticles (γ = 0.277 J/m2). Larger defect-bearing biogenic ZnS nanoparticles were thus more reactive than the smaller quantum-dot-sized ZnS nanoparticles. These findings provide new insight into the factors that affect the dissolution of metal sulfide nanoparticles in relevant natural and engineered scenarios, and have important implications for tracking the fate and transport of sulfide nanoparticles and associated metal ions in the environment. Moreover, our study exemplified the use of an in situ method (i.e., LCTEM) to investigate nanoparticle behavior (e.g., dissolution) in aqueous solutions.

Improved ZnS nanoparticle properties through sequential NanoFermentation.

Sequential NanoFermentation (SNF) is a novel process which entails sparging microbially produced gas containing H2S from a primary reactor through a concentrated metal-acetate solution contained in a secondary reactor, thereby precipitating metallic sulfide nanoparticles (e.g., ZnS, CuS, or SnS). SNF holds an advantage over single reactor nanoparticle synthesis strategies, because it avoids exposing the microorganisms to high concentrations of toxic metal and sulfide ions. Also, by segregating the nanoparticle products from biological materials, SNF avoids coating nanoparticles with bioproducts that alter their desired properties. Herein, we report the properties of ZnS nanoparticles formed from SNF as compared with ones produced directly in a primary reactor (i.e., conventional NanoFermentation, or "CNF"), commercially available ZnS, and ZnS chemically synthesized by bubbling H2S gas through a Zn-acetate solution. The ZnS nanoparticles produced by SNF provided improved optical properties due to their smaller crystallite size, smaller overall particle sizes, reduced biotic surface coatings, and reduced structural defects. SNF still maintained the advantages of NanoFermentation technology over chemical synthesis including scalability, reproducibility, and lower hazardous waste burden.

Mechanistic Investigation of Thermal and Photoreactions between Boron and Silane.

Density functional theory and high-level ab initio calculations were performed to elucidate the detailed reaction mechanism from B and SiH4 to a structure with two bridging H atoms (Si(µ-H2)BH2, silicon tetrahydroborate). On the basis of the calculated results, this reaction mechanism includes both thermal and photochemical reactions. Especially, thermal conversion of silylene dihydroborate (H2B═SiH2) to Si(µ-H2)BH2 is not feasible because two high energetic barriers must be overcome. In contrast, the reverse reaction is feasible because it is effectively only necessary to overcome a single barrier. The characteristics of the excited states of H2B═SiH2 and Si(µ-H2)BH2 have been identified. Two successive conical intersections (CIs) are involved in the photochemical reaction. The BSiH4 bending coordinate is almost parallel to the reaction coordinate near the regions from the second CI to Si(µ-H2)BH2. The activated BSiH4 bending mode lift the degeneracy of the second CI, thereby the reaction readily proceeds to Si(µ-H2)BH2. All calculated results in this work reasonably well describe the recent experimental observations.

Benchmark Study of Density Functional Theory for Neutral Gold Clusters, Aun (n = 2-8).

Neutral gold clusters, Aun (n = 2-8), were optimized using coupled cluster singles and doubles with perturbative triples (CCSD(T)) with a triple-ζ-level basis set to develop reliable reference values for their structural and energy parameters in order to assess the performance of density functionals. The performance of 44 density functional theory (DFT) methods for calculating molecular structures and relative energies is assessed with respect to CCSD(T). In addition, their performance when calculating vertical ionization potentials (vIPs) of Aun (n = 2-8) is also assessed by comparison with experimental values. The revTPSS functional shows good performance for calculating both the structural and energy properties of Aun (n = 2-8), whereas B3P86 shows a remarkable performance in calculating the vIPs. The quadruple-ζ-level valence basis set is necessary for obtaining accurate energy values in CCSD(T) calculations.

Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

Ab Initio Investigation of the Ground States of F2P(S)N, F2PNS, and F2PSN.

A recent spectroscopic experiment identified difluorothiophosphoryl nitrene (F2P(S)N) and found that it showed rich photochemistry. However, a discrepancy between the experimental results and the quantum chemical calculations was reported. Thus, high-level ab initio calculations using the coupled cluster singles and doubles with perturbative triples and second-order multiconfigurational perturbation theory were performed to elucidate this inconsistency. The discrepancy arose due to the failure to consider the triplet state of difluoro(thionitroso)phosphine (F2PNS). In this work, we identify that the global minimum of the system is the triplet state of F2PNS, which allows us to explain the inconsistency between the experimental and theoretical results. All calculated results give consistent results with the recent experimental results.

Performance of Density Functional Theory and Relativistic Effective Core Potential for Ru-Based Organometallic Complexes.

Herein a performance assessment of density functionals used for calculating the structural and energetic parameters of bi- and trimetallic Ru-containing organometallic complexes has been performed. The performance of four popular relativistic effective core potentials (RECPs) has also been assessed. On the basis of the calculated results, the MN12-SX (range-separated hybrid functional) demonstrates good performance for calculating the molecular structures, while MN12-L (local functional) performs well for calculating the energetics, including that of the Ru-Ru bond breaking process. The choice of appropriate density functional is a crucial factor for calculating the energetics. The LANL08 demonstrates the lowest performance of the RECPs for calculating the molecular structures, especially the Ru-Ru bond length.

Manufacturing demonstration of microbially mediated zinc sulfide nanoparticles in pilot-plant scale reactors.

The thermophilic anaerobic metal-reducing bacterium Thermoanaerobacter sp. X513 efficiently produces zinc sulfide (ZnS) nanoparticles (NPs) in laboratory-scale (≤ 24-L) reactors. To determine whether this process can be up-scaled and adapted for pilot-plant production while maintaining NP yield and quality, a series of pilot-plant scale experiments were performed using 100-L and 900-L reactors. Pasteurization and N2-sparging replaced autoclaving and boiling for deoxygenating media in the transition from small-scale to pilot plant reactors. Consecutive 100-L batches using new or recycled media produced ZnS NPs with highly reproducible ~2-nm average crystallite size (ACS) and yields of ~0.5 g L(-1), similar to the small-scale batches. The 900-L pilot plant reactor produced ~320 g ZnS without process optimization or replacement of used medium; this quantity would be sufficient to form a ZnS thin film with ~120 nm thickness over 0.5 m width × 13 km length. At all scales, the bacteria produced significant amounts of acetic, lactic, and formic acids, which could be neutralized by the controlled addition of sodium hydroxide without the use of an organic pH buffer, eliminating 98 % of the buffer chemical costs. The final NP products were characterized using XRD, ICP-OES, TEM, FTIR, PL, DLS, HPLC, and C/N analyses, which confirmed that the growth medium without organic buffer enhanced the ZnS NP properties by reducing carbon and nitrogen surface coatings and supporting better dispersivity with similar ACS.

Quasi-Experiment Study on Effectiveness Evaluation of Health Communication Strategies.

This experimental study examined differences in doctor-patient relationships according to the health communication strategies during cases of medical malpractices occurred at primary medical institution. A total of 116 subjects aged in their 20s-50s was sampled. The first medical malpractice scenario chosen was the medical malpractice case most frequently registered at the Korean Medical Association Mutual Aid and the second scenario was associated with materials and devices as the cause of malpractice. Four types of crisis communication strategy messages were utilized, consisting of denial, denial + ingratiation, apology, and apology + ingratiation. Subjects were classified into four research groups by crisis communication strategy to measure levels of trust, control mutuality, commitment, and satisfaction, before and after the occurrence of medical malpractice and application of communication strategies. The findings of this study revealed that the apology strategy, compared with the denial strategy, showed a smaller difference before and after the application of communication strategies in all variables of trust (F = 8.080, F = 5.768), control mutuality (F = 8.824, F = 9.081), commitment (F = 9.815, F = 8.301), and satisfaction (F = 8.723, F = 5.638). Further, a significant interaction effect was shown between variables. The apology strategy, compared with the denial strategy, was effective in the improvement of doctor-patient relationships in both Scenarios I and II. For Scenario I, the apology strategy without ingratiation boosted commitment and satisfaction, but for Scenario II, utilizing the apology strategy with ingratiation boosted the effectiveness of trust and commitment.

Theoretical Investigation of the Reaction Mechanism of the Photoisomerization of 1,2-Dihydro-1,2-azaborine.

The photoisomerization of 1,2-dihydro-1,2-azaborine was investigated by high-level multireference ab initio and density functional theory calculations. The intermediates (IMs) and transition states (TSs) on the S(0) and S(1) states were optimized using the state-averaged complete active space self-consistent field method. The multireference configuration interaction method with the Davidson correction was used to obtain accurate energetics. Moreover, the conical intersections (CIs), which play a crucial role in photoisomerization, were also optimized. On the basis of the calculation results, the most favorable proposed reaction pathway is as follows: reactant→Franck-Condon region→TS(1) →CI→IM(0) →TS(0P) →product. The product was not directly formed through the CI, and the IM(0) existed on the S(0) state. These results show that the isomerization of 1,2-dihydro-1,2-azaborine involves both photoreactions and thermal reactions. The calculated results clarify recent experimental observations.

In situ capping for size control of monochalcogenide (ZnS, CdS and SnS) nanocrystals produced by anaerobic metal-reducing bacteria.

Metal monochalcogenide quantum dot nanocrystals of ZnS, CdS and SnS were prepared by anaerobic, metal-reducing bacteria using in situ capping by oleic acid or oleylamine. The capping agent preferentially adsorbs on the surface of the nanocrystal, suppressing the growth process in the early stages, thus leading to production of nanocrystals with a diameter of less than 5 nm.

Identifying the major intermediate species by combining time-resolved X-ray solution scattering and X-ray absorption spectroscopy.

Identifying the intermediate species along a reaction pathway is a first step towards a complete understanding of the reaction mechanism, but often this task is not trivial. There has been a strong on-going debate: which of the three intermediates, the CHI2 radical, the CHI2-I isomer, and the CHI2(+) ion, is the dominant intermediate species formed in the photolysis of iodoform (CHI3)? Herein, by combining time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TR-XAS), we present strong evidence that the CHI2 radical is dominantly formed from the photolysis of CHI3 in methanol at 267 nm within the available time resolution of the techniques (∼20 ps for TRXL and ∼100 ps for TR-XAS). The TRXL measurement, conducted using the time-slicing scheme, detected no CHI2-I isomer within our signal-to-noise ratio, indicating that, if formed, the CHI2-I isomer must be a minor intermediate. The TR-XAS transient spectra measured at the iodine L1 and L3 edges support the same conclusion. The present work demonstrates that the application of these two complementary time-resolved X-ray methods to the same system can provide a detailed understanding of the reaction mechanism.

Environmental fate of the next generation refrigerant 2,3,3,3-tetrafluoropropene (HFO-1234yf).

The hydrofluoroolefin 2,3,3,3-tetrafluoropropene (HFO-1234yf) has been introduced to replace 1,1,1,2-tetrafluoroethane (HFC-134a) as refrigerant in mobile, including vehicle, air conditioning systems because of its lower global warming potential. HFO-1234yf is volatile at ambient temperatures; however, high production volumes and widespread handling are expected to release this fluorocarbon into terrestrial and aquatic environments, including groundwater. Laboratory experiments explored HFO-1234yf degradation by (i) microbial processes under oxic and anoxic conditions, (ii) abiotic processes mediated by reactive mineral phases and zerovalent iron (Fe(0), ZVI), and (iii) cobalamin-catalyzed biomimetic transformation. These investigations demonstrated that HFO-1234yf was recalcitrant to microbial (co)metabolism and no transformation was observed in incubations with ZVI, makinawite (FeS), sulfate green rust (GR(SO4)), magnetite (Fe(3)O(4)), and manganese oxide (MnO2). Sequential reductive defluorination of HFO-1234yf to 3,3,3-trifluoropropene and 3,3-dichloropropene with concomitant stoichiometric release of fluoride occurred in incubations with reduced cobalamins (e.g., vitamin B12) indicating that biomolecules can transform HFO-1234yf at circumneutral pH and at ambient temperature. Taken together, these findings suggest that HFO-1234yf recalcitrance in aquifers should be expected; however, HFO-1234yf is not inert and a biomolecule may mediate reductive transformation in low redox environments, albeit at low rates.

Oxide and 2D TMD semiconductors for 3D DRAM cell transistors.

As the downscaling of conventional dynamic random-access memory (DRAM) has reached its limits, 3D DRAM has been proposed as a next-generation DRAM cell architecture. However, incorporating silicon into 3D DRAM technology faces various challenges in securing cost-effective high cell transistor performance. Therefore, many researchers are exploring the application of next-generation semiconductor materials, such as transition oxide semiconductors (OSs) and metal dichalcogenides (TMDs), to address these challenges and to realize 3D DRAM. This study provides an overview of the proposed structures for 3D DRAM, compares the characteristics of OSs and TMDs, and discusses the feasibility of employing the OSs and TMDs as the channel material for 3D DRAM. Furthermore, we review recent progress in 3D DRAM using the OSs, discussing their potential to overcome challenges in silicon-based approaches.

Scalable economic extracellular synthesis of CdS nanostructured particles by a non-pathogenic thermophile.

We report microbially facilitated synthesis of cadmium sulfide (CdS) nanostructured particles (NP) using anaerobic, metal-reducing Thermoanaerobacter sp. The extracellular CdS crystallites were <10 nm in size with yields of ~3 g/L of growth medium/month with demonstrated reproducibility and scalability up to 24 L. During synthesis, Thermoanaerobacter cultures reduced thiosulfate and sulfite salts to H2S, which reacted with Cd²âº cations to produce thermodynamically favored NP in a single step at 65 °C with catalytic nucleation on the cell surfaces. Photoluminescence (PL) analysis of dry CdS NP revealed an exciton-dominated PL peak at 440 nm, having a narrow full width at half maximum of 10 nm. A PL spectrum of CdS NP produced by dissimilatory sulfur reducing bacteria was dominated by features associated with radiative exciton relaxation at the surface. High reproducibility of CdS NP PL features important for scale-up conditions was confirmed from test tubes to 24 L batches at a small fraction of the manufacturing cost associated with conventional inorganic NP production processes.

Ccr2+ Monocyte-Derived Macrophages Influence Trajectories of Acquired Therapy Resistance in Braf-Mutant Melanoma.

Therapies targeting oncogene addiction have had a tremendous impact on tumor growth and patient outcome, but drug resistance continues to be problematic. One approach to deal with the challenge of resistance entails extending anticancer treatments beyond targeting cancer cells by additionally altering the tumor microenvironment. Understanding how the tumor microenvironment contributes to the evolution of diverse resistance pathways could aid in the design of sequential treatments that can elicit and take advantage of a predictable resistance trajectory. Tumor-associated macrophages often support neoplastic growth and are frequently the most abundant immune cell found in tumors. Here, we used clinically relevant in vivo Braf-mutant melanoma models with fluorescent markers to track the stage-specific changes in macrophages under targeted therapy with Braf/Mek inhibitors and assessed the dynamic evolution of the macrophage population generated by therapy pressure-induced stress. During the onset of a drug-tolerant persister state, Ccr2+ monocyte-derived macrophage infiltration rose, suggesting that macrophage influx at this point could facilitate the onset of stable drug resistance that melanoma cells show after several weeks of treatment. Comparison of melanomas that develop in a Ccr2-proficient or -deficient microenvironment demonstrated that lack of melanoma infiltrating Ccr2+ macrophages delayed onset of resistance and shifted melanoma cell evolution towards unstable resistance. Unstable resistance was characterized by sensitivity to targeted therapy when factors from the microenvironment were lost. Importantly, this phenotype was reversed by coculturing melanoma cells with Ccr2+ macrophages. Overall, this study demonstrates that the development of resistance may be directed by altering the tumor microenvironment to improve treatment timing and the probability of relapse. SIGNIFICANCE: Ccr2+ melanoma macrophages that are active in tumors during the drug-tolerant persister state following targeted therapy-induced regression are key contributors directing melanoma cell reprogramming toward specific therapeutic resistance trajectories.