Isomeric Transition Research Articles

Fused 1,2,3-Thiaselenazoles Synthesized from 1,2,3-Dithiazoles through Selective Chalcogen Exchange.

A new approach to the synthesis of fused 1,2,3-thiaselenazoles-rare five-membered heterocycles that contain two different chalcogens-from the corresponding 1,2,3-dithiazoles and SeO2 was accomplished by selective exchange of S and Se atoms. The fused carbo- and heterocyclic units were indene, naphthalenone, cyclohexadienone, cyclopentadiene, benzoannulene, and benzoxazine. The molecular structures of two of the thiaselenadiazole products and one of the dithiazole precursors were confirmed by single-crystal X-ray diffraction. The reaction is highly solvent selective; it only takes place in solvents that contain a C=O group (e.g., DMF or tetramethylurea). According to DFT calculations, the reaction is thermodynamically favorable. Based on the DFT calculations and 77 Se NMR spectroscopy, two tentative mechanisms that feature isomeric transition states and intermediates are suggested for the reaction via ring-opening addition of SeO2 to the S-X dithiazole bond (X=N or S). The DFT-calculated first adiabatic electron affinities of the compounds were chalcogen independent and positive in all cases, which assumes formation of thermodynamically stable radical anions (RAs). These calculated RAs featured either normal or abnormal elongation of the S1-X2 (X=S or Se) bond relative to their neutral precursors and possessed π* or σ* SOMOs, respectively.

Molecular Isomerization and Multiscale Phase Transitions of a Ditopic Ligand on a Surface

A multiscale irreversible phase transition of a ditopic ligand on a surface has been investigated by scanning tunneling microscopy. The phase transitions, which are generated by protonation, involve an intramolecular cis- to trans-like isomerization, a change from weak to strong hydrogen bonding, and a structural phase transformation of gear chains into a stripe-like organization.

Loading of mass spectrometry ion trap with Th ions by laser ablation for nuclear frequency standard application.

We describe an original multisectional quadrupole ion trap aimed to realize nuclear frequency standard based on the unique isomer transition in thorium nucleus. It is shown that the system effectively operates on Th+, Th2+ and Th3+ ions produced by laser ablation of metallic thorium-232 target. Laser intensity used for ablation is about 6 GW/cm2. Via applying a bias potential to every control voltage including the RF one, we are able not only to manipulate ions within the energy range as wide as 1-500 eV but to specially adjust trap potentials in order to work mainly with ions that belong to energy distribution maximum and therefore to effectively enhance the number of trapped ions. Measurement of energy distributions of 232Th+, 232Th2+, 232Th3+ ions obtained by laser ablation allows us to define optimal potential values for trapping process. Observed number of ions inside trap in dependence on trapping time is found to obey an unusually slow - logarithmic decay law that needs more careful study.

Radical Reactions Affecting Polar Groups in Threonine Peptide Ions.

Peptide cation-radicals containing the threonine residue undergo radical-induced dissociations upon collisional activation and photon absorption in the 210-400 nm range. Peptide cation-radicals containing a radical defect at the N-terminal residue, [•Ala-Thr-Ala-Arg+H]+, were generated by electron transfer dissociation (ETD) of peptide dications and characterized by UV-vis photodissociation action spectroscopy combined with time-dependent density functional theory (TD-DFT) calculations of absorption spectra, including thermal vibronic band broadening. The action spectrum of [•Ala-Thr-Ala-Arg+H]+ ions was indicative of the canonical structure of an N-terminally deaminated radical whereas isomeric structures differing in the position of the radical defect and amide bond geometry were excluded. This indicated that exothermic electron transfer to threonine peptide ions did not induce radical isomerizations in the fragment cation-radicals. Several isomeric structures, ion-molecule complexes, and transition states for isomerizations and dissociations were generated and analyzed by DFT and Møller-Plesset perturbational ab initio calculations to aid interpretation of the major dissociations by loss of water, hydroxyl radical, C3H6NO•, C3H7NO, and backbone cleavages. Born-Oppenheimer molecular dynamics (BOMD) in combination with DFT gradient geometry optimizations and intrinsic reaction coordinate analysis were used to search for low-energy cation-radical conformers and transition states. BOMD was also employed to analyze the reaction trajectory for loss of water from ion-molecule complexes.

Possible mantle phase transitions by the formation of SiO2 peroxides: Implications for mantle convection

On the basis of quantum–chemical calculations of the linear to isomeric bent transition of the SiO2 molecule, it is suggested that the bent to linear transition of SiO2 forms can occur in melted mantle minerals of the lower mantle. This may be important for the formation of the peculiarities of mantle convection and origination of plumes.

Pressure-dependent kinetics on the C4H7 potential energy surface and its effect on combustion model predictions

Butene (C4H8), the smallest alkene possessing both branched and straight-chain isomers, is usually an important intermediate with relatively high concentration in the combustion of hydrocarbons and oxygenated fuels. In the present study, the kinetics of thermal isomerization, decomposition and chemical activation reactions of three typical butenyl isomers, i.e. nC4H7 (CH2=CHCH2ĊH2), saxC4H7 (CH2=CHĊHCH3) and iC4H7 (CH2=C(CH3)ĊH2), were systematically investigated by theoretical calculations. High-level ab initio calculations coupled with the RRKM/master equation method were used to compute the temperature and pressure dependent rate coefficients. The results show that the existence of vinylic CC bond in iC4H7 largely impedes its decomposition rate. The transformation from iC4H7 to straight-chain C4H7 is kinetically unfavorable due to the high strain energy of the 3-membered ring structure of the isomerization transition state. Furthermore, the calculated rate coefficients were incorporated into USC Mech II and Aramco Mech 2.0 to examine the impact of our computed pressure-dependent kinetics on model predictions. Although the simulation results demonstrate limited improvement on ignition delay time and laminar flame speed of butene, substantial changes are observed for the mole fractions of important intermediate species, e.g., allene and 1,3-butediene, in butene pyrolysis. Modified Arrhenius representations of the calculated rate constants are given and should be used in combustion modeling.

Electrostatic Control of Regioselectivity in Au(I)-Catalyzed Hydroarylation.

Competing pathways in catalytic reactions often involve transition states with very different charge distributions, but this difference is rarely exploited to control selectivity. The proximity of a counterion to a charged catalyst in an ion paired complex gives rise to strong electrostatic interactions that could be used to energetically differentiate transition states. Here we investigate the effects of ion pairing on the regioselectivity of the hydroarylation of 3-substituted phenyl propargyl ethers catalyzed by cationic Au(I) complexes, which forms a mixture of 5- and 7-substituted 2H-chromenes. We show that changing the solvent dielectric to enforce ion pairing to a SbF6- counterion changes the regioselectivity by up to a factor of 12 depending on the substrate structure. Density functional theory (DFT) is used to calculate the energy difference between the putative product-determining isomeric transition states (ΔΔE‡) in both the presence and absence of the counterion. The change in ΔΔE‡ upon switching from the unpaired transition states in high solvent dielectric to ion paired transition states in low solvent dielectric (Δ(ΔΔE‡)) was found to be in good agreement with the experimentally observed selectivity changes across several substrates. Our calculations indicate that the origin of Δ(ΔΔE‡) lies in the preferential electrostatic stabilization of the transition state with greater charge separation by the counterion in the ion paired case. By performing calculations at multiple different values of the solvent dielectric, we show that the role of the solvent in changing selectivity is not solely to enforce ion pairing, but rather that interactions between the ion paired complex and the solvent also contribute to Δ(ΔΔE‡). Our results provide a foundation for exploiting electrostatic control of selectivity in other ion paired systems.

Verification of the databases EXFOR and ENDF

The objective of this work is for the verification of large experimental (EXFOR) and evaluated nuclear reaction databases (JEFF, ENDF, JENDL, TENDL…). The work is applied to neutron reactions in EXFOR data, including threshold reactions, isomeric transitions, angular distributions and data in the resonance region of both isotopes and natural elements. Finally, a comparison of the resonance integrals compiled in EXFOR database with those derived from the evaluated libraries is also performed.

Thorium silicate compound as a solid-state target for production of isomeric thorium-229 nuclei by electron beam irradiation

In this paper, we discuss an idea of the experiment for excitation of the isomeric transition in thorium-229 nuclei by irradiating with electron beam targets with necessary physical characteristics. The chemical composition and bandgap of ThSi10O22 were determined by X-ray photoelectron spectroscopy and reflection electron energy loss spectroscopy. It was found that the energy gap is equal to 7.7 eV and does not change when the target is exposed to a medium energy electron beam for a long time. This indicates that the compound possesses high electron-beam resistance. A quantitative estimation of the output function of isomeric thorium-229 nuclei generated by interaction of nuclei with the secondary electron flow formed by irradiating the solid-state ThSi10O22-based target is given. The estimation shows that ThSi10O22 is a promising thorium-containing target for investigating excitation of the nuclear low-lying isomeric transition in the thorium-229 isotope using medium-energy electrons.

Scheme of the β-decay of 234Th

The scheme of the β-decay of 234Th is still not completely clear. Only the upper bound (10 keV) of the energy of the isomeric transition from level T1/2 = 1.17 min of the 234Pa nucleus is known, and the correspondence between gamma quanta of several energies emitted in the β-decay of 234Th and specific nuclear levels of 234Pa has not been established. In this work, the isomeric transition energy of 2.6 ± 0.5 keV is determined via the γ-spectrometry of a 234Th source in γγ-coincidences, and a new 234Pa level populated in the β-decay of 234Th is introduced.

Anomalous magnetic hyperfine structure of theTh229ground-state doublet in muonic atoms

The hyperfine splitting of the ground and low-energy $3/2^+(7.8 \pm 0.5$ eV) levels in the $^{229}$Th nucleus in muonic atom ($\mu^-_{1S_{1/2}}{}^{229}$Th$)^*$ has been calculated considering the distribution of the nuclear magnetization in the framework of collective nuclear model with the wave functions of the Nilsson model for the unpaired neutron. It is shown that (a) the hyperfine splitting of the $3/2^+$ isomeric state is anomalously weak, and the reduction of hyperfine structure in comparison with the model of a point nuclear magnetic dipole is close to 100\%, (b) partial inversion of levels of the $^{229}$Th ground-state doublet and spontaneous decay of the ground state with excitation of the isomeric state take place, (c) the energy of the isomeric transition lies in the range of 120--140 eV, which makes possible the direct observation of the transition, registration of conversion electrons and measurement of the nuclear matrix element.

Photoinduced and Thermal Relaxation in Surface-Grafted Azobenzene-Based Monolayers: A Molecular Dynamics Simulation Study.

Extensive atomistic molecular dynamics simulations have been employed to study the structure and molecular orientational relaxation of azobenzene-based monolayers grafted to a solid substrate. Systems with surface coverage of 0.6 nm(2)/molecule were investigated over a wide temperature range ranging from 298 K, where the mesogens show local ordering and the monolayer dynamics was found to be glassy, up to 700 K, where the azobenzene groups have a nearly isotropic orientational distribution, with a subnanosecond characteristic orientational relaxation time scale. Biased simulations that model single-molecule thermal excitation and conformational isomerization have been conducted to obtain insight into the mechanisms for photoinduced athermal fluidization and monolayer reorganization observed experimentally in this system. Our simulations clearly indicate that trans-cis conformational isomerization transitions of azobenzene units can lead to reorientation of mesogens and to the formation of a monolayer with strong macroscopic in-plane nematic order. While local heating created by excitation process can facilitate this process, thermal excitation alone is not sufficient to induce ordering in the monolayer. Instead, the work done by a molecule undergoing cis-trans isomerization on the cage of neighboring molecules is the key mechanism for photofluidization and orientational ordering in dMR monolayers exposed to linearly polarized light leading to relaxation dynamics that can be described in terms of higher effective temperature. The obtained simulation results are discussed in light of recent experimental data reported for these systems.

A VUV detection system for the direct photonic identification of the first excited isomeric state of 229Th

With an expected energy of 7.6(5) eV, $^{229}$Th possesses the lowest excited nuclear state in the landscape of all presently known nuclei. The energy corresponds to a wavelength of about 160 nm and would conceptually allow for an optical laser excitation of a nuclear transition. We report on a VUV optical detection system that was designed for the direct detection of the isomeric ground-state transition of $^{229}$Th. $^{229(m)}$Th ions originating from a $^{233}$U $\alpha$-recoil source are collected on a micro electrode that is placed in the focus of an annular parabolic mirror. The latter is used to parallelize the UV fluorescence that may emerge from the isomeric ground-state transition of $^{229}$Th. The parallelized light is then focused by a second annular parabolic mirror onto a CsI-coated position-sensitive MCP detector behind the mirror exit. To achieve a high signal-to-background ratio, a small spot size on the MCP detector needs to be achieved. Besides extensive ray-tracing simulations of the optical setup, we present a procedure for its alignment, as well as test measurements using a D$_2$ lamp, where a focal-spot size of $\approx$100 $\mu$m has been achieved. Assuming a purely photonic decay, a signal-to-background ratio of $\approx$7000:1 could be achieved.

Electronic Spectra of Protonated Fluoranthene in a Neon Matrix and Gas Phase at 10 K.

Four electronic systems with origin bands at 759.5, 559.3, 476.3, and 385.5 nm are detected in a 6 K neon matrix following deposition of mass-selected protonated fluoranthene C16H11(+) produced from a reaction of neutral vapor and ethanol in a hot-cathode ion source. Two cationic isomers are identified as the carriers of these band systems. The 559.3, 476.3, and 385.5 nm absorptions are assigned to 4,3,2 (1)A' ← X (1)A' transitions of isomer E(+) (γ-) and the 2 (1)A' ← X (1)A' system at 759.5 nm is of isomer C(+) (α-) of protonated fluoranthene on the basis of theoretical predictions. The electronic spectrum of E(+) was also recorded in the gas phase using a resonant 1 + 1 two-photon excitation-dissociation technique in an ion trap at vibrational and rotational temperatures of 10 K. The 3,2 (1)A' ← X (1)A' transitions have origin band maxima at 558.28 ± 0.01 and 474.92 ± 0.01 nm. Both the 2 (1)A' and 3 (1)A' excited states have a distinct vibrational pattern with lifetimes on the order of 1 ps.

Titration and quantification of open and closed Lewis acid sites in Sn-Beta zeolites that catalyze glucose isomerization

Methods to quantify framework Lewis acidic Sn4+ sites in zeolite Beta (Sn-Beta) with four Lewis base titrants (pyridine, deuterated acetonitrile, n-propylamine, ammonia) were developed using infrared (IR) spectroscopy or temperature programmed desorption (TPD). Integrated molar extinction coefficients (E, cmμmol−1) were measured for IR bands of pyridine adsorbed to Lewis acidic Sn sites (E(1450cm−1)=1.42±0.30) and of CD3CN adsorbed to open (E(2316cm−1)=1.04±0.22) and closed (E(2308cm−1)=2.04±0.43) Sn sites, and differ from analogous E values for Lewis acidic Al sites by up to 3.6×. TPD of Sn-Beta samples after saturation with NH3 or n-propylamine (NPA) and purging to remove physisorbed species also enabled quantification of Lewis acid sites, which is seldom performed despite analogous methods that use such titrants to quantify Brønsted sites in solid acids. These four Lewis bases titrated Lewis acidic Sn sites with equimolar stoichiometry and counted similar numbers of Sn sites on low-defect Sn-Beta samples synthesized in fluoride media (Sn-Beta-F) with high Sn content (Si/Sn <150). NPA binding on residual silanol defect sites, however, caused overestimation of Sn sites by TPD on Sn-Beta-F samples with low Sn content (Si/Sn >175) or high defect Sn-Beta samples prepared via post-synthetic insertion of Sn atoms into framework vacancy defects of dealuminated Beta zeolites (Sn-Beta-OH). Molar ratios of open-to-closed Sn sites varied widely (0.29–1.64) among the eight Sn-Beta samples studied here. Open Sn sites have been proposed as the dominant active sites for aqueous-phase glucose–fructose isomerization via intramolecular 1,2-hydride shift, consistent with successive poisoning of Sn-Beta samples with pyridine prior to measurement of initial glucose isomerization rates that suppressed reactivity at pyridine uptakes similar to the number of open Sn sites counted ex-situ by CD3CN. Measured first-order glucose isomerization rate constants in water (per open Sn, 373K), which reflect free energy differences between isomerization transition states and two coordinated water molecules at Sn sites, were ∼50× higher on hydrophobic Sn-Beta-F than on hydrophilic Sn-Beta-OH zeolites. The characterization methods reported herein enable normalization of initial glucose isomerization turnover rates on Sn-Beta zeolites by their number of open Sn sites, as required prior to interpreting the catalytic consequences of structural heterogeneities introduced by differences in sample preparation or treatment history.

Phosphorylation/Dephosphorylation Assays.

The P-type ATPases form an autophosphorylated intermediate with ATP, and its isomeric transition and hydrolysis are obligatory events in the ATP-driven pump and thus for the energy coupling. The analyses of these reactions are therefore crucial for understanding the mechanism of the pump function and diseases caused by its defects. Here we describe the methods to analyze these processes in the transport cycle with a representative member of P-type ATPase family, SERCA1a, sarco(endo)plasmic reticulum Ca(2+)-ATPase.

Spectroscopic characterization of isomerization transition states.

Transition state theory is central to our understanding of chemical reaction dynamics. We demonstrate a method for extracting transition state energies and properties from a characteristic pattern found in frequency-domain spectra of isomerizing systems. This pattern-a dip in the spacings of certain barrier-proximal vibrational levels-can be understood using the concept of effective frequency, ω(eff). The method is applied to the cis-trans conformational change in the S1 state of C2H2 and the bond-breaking HCN-HNC isomerization. In both cases, the barrier heights derived from spectroscopic data agree extremely well with previous ab initio calculations. We also show that it is possible to distinguish between vibrational modes that are actively involved in the isomerization process and those that are passive bystanders.

Radioluminescence and photoluminescence of Th:CaF2 crystals.

We study thorium-doped CaF2 crystals as a possible platform for optical spectroscopy of the 229Th nuclear isomer transition. We anticipate two major sources of background signal that might cover the nuclear spectroscopy signal: VUV-photoluminescence, caused by the probe light, and radioluminescence, caused by the radioactive decay of 229Th and its daughters. We find a rich photoluminescence spectrum at wavelengths above 260 nm, and radioluminescence emission above 220 nm. This is very promising, as fluorescence originating from the isomer transition, predicted at a wavelength shorter than 200 nm, could be filtered spectrally from the crystal luminescence. Furthermore, we investigate the temperature-dependent decay time of the luminescence, as well as thermoluminescence properties. Our findings allow for an immediate optimization of spectroscopy protocols for both the initial search for the nuclear transition using synchrotron radiation, as well as future optical clock operation with narrow-linewidth lasers.

Quantum-Chemical Calculation of Carbododecahedron Formation in Carbon Plasma.

The ground state of the molecule consisting of 10 carbon atoms in C10(rg) "ring" conformation and the energy of its metastable C10(st) "star" conformation are reported. The reaction coordinate for the isomeric transition C10(st) → C10(rg) was calculated using density functional theory (DFT) with UB3LYP/6-31G(d,p). It was established that a 5-fold symmetry axis is conserved in this isomeric transition. The total energy of the ring isomer is by 10.33 eV (9.16 eV as zero-point energy corrected) lower than that of the star isomer. The energy barrier for the transition from the metastable star state to the ring state is 2.87 eV (3.57 eV as zero-point energy corrected). An analysis of possible chemical reactions in carbon plasma involving C10(st) and C10(rg) and leading to the formation of C20 fullerenes was performed. It was revealed that the presence of the C10(st) conformation in the reaction medium is a necessary condition for C20 fullerene formation. It was shown that the presence of hydrogen atoms in carbon plasma and UV radiation accelerate the C10(st) → C10(rg) transition and thus suppress the C20 fullerene formation.

An estimate of energy of isomeric transition in the decay of 234m Pa

Experimental data on the decay of 234Th and the forbiddenness factors of the E3 transitions in neighboring nuclei suggest that the energy of the isomeric E3 transition in the decay of 234m Pa is ≈50 eV.