Electronic Structures and Spectroscopic Signatures of Noble-Gas-Doped Nanodiamonds
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ABSTRACT:
SUBMITTER: Beck R
PROVIDER: S-EPMC10214509 | biostudies-literature | 2023 Feb
REPOSITORIES: biostudies-literature
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Project description:Oganesson (Og) is the last entry into the Periodic Table completing the seventh period of elements and group 18 of the noble gases. Only five atoms of Og have been successfully produced in nuclear collision experiments, with an estimate half-life for 294118 Og of 0. 69+0.64-0.22 ms.[1] With such a short lifetime, chemical and physical properties inevitably have to come from accurate relativistic quantum theory. Here, we employ two complementary computational approaches, namely parallel tempering Monte-Carlo (PTMC) simulations and first-principles thermodynamic integration (TI), both calibrated against a highly accurate coupled-cluster reference to pin-down the melting and boiling points of this super-heavy element. In excellent agreement, these approaches show Og to be a solid at ambient conditions with a melting point of ≈325 K. In contrast, calculations in the nonrelativistic limit reveal a melting point for Og of 220 K, suggesting a gaseous state as expected for a typical noble gas element. Accordingly, relativistic effects shift the solid-to-liquid phase transition by about 100 K.
| S-EPMC7814676 | biostudies-literature
Project description:We have designed a new type of molecule with a noble gas (Ng = Kr and Xe) atom in a six-membered ring. Their structures and stability have been studied by density functional theory and by correlated electronic structure calculations. The results showed that the six-membered ring is planar with very short Ng-O and Ng-N polar covalent bonds. The calculated energy barriers for all the unimolecular dissociation pathways are higher than 20 and 35 kcal/mol for Ng = Kr and Xe, respectively. The current study suggests that these molecules and their derivatives might be synthesized and observable at cryogenic conditions.
| S-EPMC8347956 | biostudies-literature
Project description:The activation of O2 at thiolate-ligated iron(II) sites is essential to the function of numerous metalloenzymes and synthetic catalysts. Iron-thiolate bonds in the active sites of nonheme iron enzymes arise from either coordination of an endogenous cysteinate residue or binding of a deprotonated thiol-containing substrate. Examples of the latter include sulfoxide synthases, such as EgtB and OvoA, that utilize O2 to catalyze tandem S-C bond formation and S-oxygenation steps in thiohistidine biosyntheses. We recently reported the preparation of two mononuclear nonheme iron-thiolate complexes (1 and 2) that serve as structural active-site models of substrate-bound EgtB and OvoA (Dalton Trans. 2020, 49, 17745-17757). These models feature monodentate thiolate ligands and tripodal N4 ligands with mixed pyridyl/imidazolyl donors. Here, we describe the reactivity of 1 and 2 with O2 at low temperatures to give metastable intermediates (3 and 4, respectively). Characterization with multiple spectroscopic techniques (UV-vis absorption, NMR, variable-field and -temperature Mössbauer, and resonance Raman) revealed that these intermediates are thiolate-ligated iron(III) dimers with a bridging oxo ligand derived from the four-electron reduction of O2. Structural models of 3 and 4 consistent with the experimental data were generated via density functional theory (DFT) calculations. The combined experimental and computational results illuminate the geometric and electronic origins of the unique spectral features of diiron(III)-μ-oxo complexes with thiolate ligands, and the spectroscopic signatures of 3 and 4 are compared to those of closely-related diiron(III)-μ-peroxo species. Collectively, these results will assist in the identification of intermediates that appear on the O2 reaction landscapes of iron-thiolate species in both biological and synthetic environments.
| S-EPMC8721859 | biostudies-literature
Project description:Using interwoven experimental and theoretical methods, detailed studies of several structurally defined 1:1 Cu-O 2 complexes have provided important fundamental chemical information useful for understanding the nature of intermediates involved in aerobic oxidations in synthetic and enzymatic copper-mediated catalysis. In particular, these studies have shed new light on the factors that influence the mode of O 2 coordination (end-on vs side-on) and the electronic structure, which can vary between Cu(II)-superoxo and Cu(III)-peroxo extremes.
| S-EPMC2593863 | biostudies-literature
Project description:Recent development in the synthesis and characterization of noble-gas compounds is reviewed, i.e., noble-gas chemistry reported in the last five years with emphasis on the publications issued after 2017. XeF2 is commercially available and has a wider practical application both in the laboratory use and in the industry. As a ligand it can coordinate to metal centers resulting in [M(XeF2)x]n+ salts. With strong Lewis acids, XeF2 acts as a fluoride ion donor forming [XeF]+ or [Xe2F3]+ salts. Latest examples are [Xe2F3][RuF6]·XeF2, [Xe2F3][RuF6] and [Xe2F3][IrF6]. Adducts NgF2·CrOF4 and NgF2·2CrOF4 (Ng = Xe, Kr) were synthesized and structurally characterized at low temperatures. The geometry of XeF6 was studied in solid argon and neon matrices. Xenon hexafluoride is a well-known fluoride ion donor forming various [XeF5]+ and [Xe2F11]+ salts. A large number of crystal structures of previously known or new [XeF5]+ and [Xe2F11]+ salts were reported, i.e., [Xe2F11][SbF6], [XeF5][SbF6], [XeF5][Sb2F11], [XeF5][BF4], [XeF5][TiF5], [XeF5]5[Ti10F45], [XeF5][Ti3F13], [XeF5]2[MnF6], [XeF5][MnF5], [XeF5]4[Mn8F36], [Xe2F11]2[SnF6], [Xe2F11]2[PbF6], [XeF5]4[Sn5F24], [XeF5][Xe2F11][CrVOF5]·2CrVIOF4, [XeF5]2[CrIVF6]·2CrVIOF4, [Xe2F11]2[CrIVF6], [XeF5]2[CrV2O2F8], [XeF5]2[CrV2O2F8]·2HF, [XeF5]2[CrV2O2F8]·2XeOF4, A[XeF5][SbF6]2 (A = Rb, Cs), Cs[XeF5][BixSb1-xF6]2 (x = ~0.37-0.39), NO2XeF5(SbF6)2, XeF5M(SbF6)3 (M = Ni, Mg, Zn, Co, Cu, Mn and Pd) and (XeF5)3[Hg(HF)]2(SbF6)7. Despite its extreme sensitivity, many new XeO3 adducts were synthesized, i.e., the 15-crown adduct of XeO3, adducts of XeO3 with triphenylphosphine oxide, dimethylsulfoxide and pyridine-N-oxide, and adducts between XeO3 and N-bases (pyridine and 4-dimethylaminopyridine). [Hg(KrF2)8][AsF6]2·2HF is a new example of a compound in which KrF2 serves as a ligand. Numerous new charged species of noble gases were reported (ArCH2+, ArOH+, [ArB3O4]+, [ArB3O5]+, [ArB4O6]+, [ArB5O7]+, [B12(CN)11Ne]-). Molecular ion HeH+ was finally detected in interstellar space. The discoveries of Na2He and ArNi at high pressure were reported. Bonding motifs in noble-gas compounds are briefly commented on in the last paragraph of this review.
| S-EPMC7412050 | biostudies-literature
Project description:The structures and spectral features of protonated noble gas clusters are examined using a first principles approach. Protonated noble gas monomers (NgH+) and dimers (NgH+Ng) have a linear structure, while the protonated noble gas trimers (Ng3H+) can have a T-shaped or linear structure. Successive binding energies for these complexes are calculated at the CCSD(T)/CBS level of theory. Anharmonic simulations for the dimers and trimers unveil interesting spectral features. The symmetric NgH+Ng are charactized by a set of progression bands, which involves one quantum of the asymmetric Ng-H+ stretch with multiple quanta of the symmetric Ng-H+ stretch. Such a spectral signature is very robust and is predicted to be observed in both T-shaped and linear isomers of Ng3H+. Meanwhile, for selected asymmetric NgH+Ng', a Fermi resonance interaction involving the first overtone of the proton bend with the proton stretch is predicted to occur in ArH+Kr and XeH+Kr.
| S-EPMC9143425 | biostudies-literature
Project description:Noble gases, especially xenon (Xe), have been shown to have antiapoptotic effects in treating hypoxia ischemia related injuries. Currently, in vivo gas delivery is systemic and performed through inhalation, leading to reduced efficacy at the injury site. This report provides a first demonstration of the encapsulation of pure Xe, Ar, or He in phospholipid-coated sub-10 µm microbubbles, without the necessity of stabilizing perfluorocarbon additives. Optimization of shell compositions and preparation techniques show that distearoylphosphatidylcholine (DSPC) with DSPE-PEG5000 can produce stable microbubbles upon shaking, while dibehenoylphosphatidylcholine (DBPC) blended with either DSPE-PEG2000 or DSPE-PEG5000 produces a high yield of microbubbles via a sonication/centrifugation method. Xe and Ar concentrations released into the microbubble suspension headspace are measured using GC-MS, while Xe released directly in solution is detected by the fluorescence quenching of a Xe-sensitive cryptophane molecule. Bubble production is found to be amenable to scale-up while maintaining their size distribution and stability. Excellent ultrasound contrast is observed in a phantom for several minutes under physiological conditions, while an intravenous administration of a bolus of pure Xe microbubbles provides significant contrast in a mouse in pre- and post-lung settings (heart and kidney, respectively), paving the way for image-guided, localized gas delivery for theranostic applications.
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Project description:Silicon carbide (SiC) is recognized as excellent material for high power/temperature applications with a wide-band gap semiconductor. With different structures at the nanosize scale, SiC nanomaterials offer outstanding mechanical, physical, and chemical properties leading to a variety of applications. In this work, new 3D pillared SiC nanostructures have been designed and investigated based on self-consistent charge density functional tight-binding (SCC-DFTB) including Van der Waals dispersion corrections. The structural and electronic properties of 3D pillared SiC nanostructures with effects of diameters and pillar lengths have been studied and compared with 3D pillared graphene nanostructures. The permeability of small gas molecules including H2O, CO2, N2, NO, O2, and NO2 have been demonstrated with different orientations into the 3D pillared SiC nanostructures. The promising candidate of 3D pillared SiC nanostructures for gas molecule separation application at room temperature is highlighted.
| S-EPMC9182379 | biostudies-literature
Project description:Vitamin B(12) (cyanocobalamin) and its biologically active derivatives, methylcobalamin and adenosylcobalamin, are members of the family of corrinoids, which also includes cobinamides. As biological precursors to cobalamins, cobinamides possess the same structural core, consisting of a low-spin Co(3+) ion that is ligated equatorially by the four nitrogens of a highly substituted tetrapyrrole macrocycle (the corrin ring), but differ with respect to the lower axial ligation. Specifically, cobinamides possess a water molecule instead of the nucleotide loop that coordinates axially to Co(3+)cobalamins via its dimethylbenzimidazole (DMB) base. Compared to the cobalamin species, cobinamides have proven much more difficult to study experimentally, thus far eluding characterization by X-ray crystallography. In this study, we have utilized combined quantum mechanics/molecular mechanics (QM/MM) computations to generate complete structural models of a representative set of cobinamide species with varying upper axial ligands. To validate the use of this approach, analogous QM/MM geometry optimizations were carried out on entire models of the cobalamin counterparts for which high-resolution X-ray structural data are available. The accuracy of the cobinamide structures was assessed further by comparing electronic absorption spectra computed using time-dependent density functional theory to those obtained experimentally. Collectively, the results obtained in this study indicate that the DMB ? H(2)O lower axial ligand switch primarily affects the energies of the Co 3d(z(2))-based molecular orbital (MO) and, to a lesser extent, the other Co 3d-based MOs as well as the corrin ?-based highest energy MO. Thus, while the energy of the lowest-energy electronic transition of cobalamins changes considerably as a function of the upper axial ligand, it is nearly invariant for the cobinamides.
| S-EPMC4656031 | biostudies-literature
Project description:The unique capacity of localized surface plasmon resonance (LSPR) offers a new opportunity to overcome the limited efficiency of semiconductor photocatalyst. Here we unravel that LSPR, which usually occurs in noble metal nanoparticles, can be realized by hydrogen doping in noble-metal-free semiconductor using TiO2 as a model photocatalyst. Moreover, its LSPR is located in infrared region, which supplements that of noble metal whose LSPR is generally in the visible region, making it possible to extend the light response of photocatalyst to infrared region. The near field enhancement is shown to be comparable with that of noble-metal nanoparticles, indicating that highly enhanced light absorption rate can be expected. The present work can provide a key guideline for the creation of highly efficient noble-metal-free plasmonic photocatalysts and have a much wider impact in infrared bioimaging and spectroscopy where infrared LSPR is essential.
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