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Zatsepin, Pavel,Ahn, Seihwan,Pudasaini, Bimal,Gau, Michael R.,Baik, Mu-Hyun,Mindiola, Daniel J. The Royal Society of Chemistry 2019 Chemical communications Vol.55 No.13
<P>Cp*(Me3P)Ir(CH3)(OTf), a complex known to reversibly activate CH4 and other hydrocarbons under mild conditions, reacts with the phosphorus ylide H2CPPh3 in THF to afford two major species [Cp*(Me3P)(Ph3P)Ir(CH2CH3)][OTf] and [Cp*(Me3P)Ir(H)(η<SUP>2</SUP>-CH2CH2)][OTf]. Insertion of the ylide methylene group can also occur with Cp*(Me3P)Ir(Ph)(OTf) to afford the benzyl [Cp*(Me3P)(Ph3P)Ir(CH2Ph)][OTf]. Theoretical studies suggest the intermediacy of an Ir(iii)CH2 species.</P>
Leedahl, B.,Zatsepin, D. A.,Boukhvalov, D. W.,Kurmaev, E. Z.,Green, R. J.,Zhidkov, I. S.,Kim, S. S.,Cui, L.,Gavrilov, N. V.,Cholakh, S. O.,Moewes, A. American Chemical Society 2014 The Journal of Physical Chemistry Part C Vol.118 No.48
<P>Herein we systematically study a range of dopants (Cr, Fe, Ni, Cu, and an MnCo alloy) in ZnO and TiO<SUB>2</SUB> using several X-ray spectroscopic techniques. We identify the dopant’s local environment and interaction with the host lattice by employing crystal field multiplet calculations and hence clarify their potential applicability for spintronic technologies. Our density functional theory (DFT) calculations predict a decreasing probability of direct cation (Zn/Ti) substitution by dopant atoms as atomic number increases, as well as a much greater likelihood of metallic clustering in TiO<SUB>2</SUB>. Our spectroscopic measurements confirm that in all cases, except Mn, metallic clusters of dopant atoms form in the TiO<SUB>2</SUB> crystal lattice, thus making it unfit for spintronic capabilities. On the other hand, in ZnO, the dopants substitute directly into zinc sites, which is promising for spintronic technologies.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpccck/2014/jpccck.2014.118.issue-48/jp509761c/production/images/medium/jp-2014-09761c_0011.gif'></P>
Structural defects induced by Fe-ion implantation in TiO<sub>2</sub>
Leedahl, B.,Zatsepin, D. A.,Boukhvalov, D. W.,Green, R. J.,McLeod, J. A.,Kim, S. S.,Kurmaev, E. Z.,Zhidkov, I. S.,Gavrilov, N. V.,Cholakh, S. O.,Moewes, A. American Institute of Physics 2014 Journal of Applied Physics Vol.115 No.5
X-ray photoelectron spectroscopy and resonant x-ray emission spectroscopy measurements of pellet and thin film forms of TiO2 with implanted Fe ions are presented and discussed. The findings indicate that Fe-implantation in a TiO2 pellet sample induces heterovalent cation substitution (Fe2+ -> Ti4+) beneath the surface region. But in thin film samples, the clustering of Fe atoms is primarily detected. In addition to this, significant amounts of secondary phases of Fe3+ are detected on the surface of all doped samples due to oxygen exposure. These experimental findings are compared with density functional theory calculations of formation energies for different configurations of structural defects in the implanted TiO2:Fe system. According to our calculations, the clustering of Fe-atoms in TiO2:Fe thin films can be attributed to the formation of combined substitutional and interstitial defects. Further, the differences due to Fe doping in pellet and thin film samples can ultimately be attributed to different surface to volume ratios. (C) 2014 AIP Publishing LLC.
Time-resolved serial femtosecond X-ray crystallography
이지혜,Nadia A. Zatsepin,김경현 한국구조생물학회 2018 Biodesign Vol.6 No.1
Time-resolved serial femtosecond crystallography (TR-SFX) with X-ray free electron lasers (XFELs) is a powerful newtechnique for the study of protein dynamics on unprecedented time scales, at room temperature, without structureaffectingradiation damage. The construction of Pohang Accelerator Laboratory XFEL, a 0.1-nm hard X-ray free-electronlaser facility based on a 10-GeV S-band linear accelerator in Pohang, Korea, provides a great opportunity to exploit anddevelop this novel methodology for structural biological studies. This review summarizes the state of the art in TR-SFXincluding key contributions of pump-probe and mix-and-inject TR-SFX to the field of protein dynamics.
Local Structure of Fe Impurity Atoms in ZnO: Bulk versus Surface
McLeod, J. A.,Boukhvalov, D. W.,Zatsepin, D. A.,Green, R. J.,Leedahl, B.,Cui, L.,Kurmaev, E. Z.,Zhidkov, I. S.,Finkelstein, L. D.,Gavrilov, N. V.,Cholakh, S. O.,Moewes, A. American Chemical Society 2014 The Journal of Physical Chemistry Part C Vol.118 No.10
<P>By studying Fe-doped ZnO pellets and thin films with various X-ray spectroscopic techniques, and complementing this with density functional theory calculations, we find that Fe-doping in bulk ZnO induces isovalent (and isostructural) cation substitution (Fe<SUP>2+</SUP> → Zn<SUP>2+</SUP>). In contrast to this, Fe-doping near the surface produces both isovalent and heterovalent substitution (Fe<SUP>3+</SUP> → Zn<SUP>2+</SUP>). The calculations performed herein suggest that the most likely defect structure is the single or double substitution of Zn with Fe, although, if additional oxygen is available, then Fe substitution with interstitial oxygen is even more energetically favorable. Furthermore, it is found that ferromagnetic states are energetically unfavorable, and ferromagnetic ordering is likely to be realized only through the formation of a secondary phase (i.e., ZnFe<SUB>2</SUB>O<SUB>4</SUB>), or codoping with Cu.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpccck/2014/jpccck.2014.118.issue-10/jp411219z/production/images/medium/jp-2013-11219z_0010.gif'></P>
Green, R.J.,Hunt, A.,Zatsepin, D.A.,Boukhvalov, D.W.,McLeod, J.A.,Kurmaev, E.Z.,Skorikov, N.A.,Gavrilov, N.V.,Moewes, A. North-Holland 2012 Journal of non-crystalline solids Vol.358 No.23
The electronic structures of Sn and Pb implanted SiO<SUB>2</SUB> are studied using soft X-ray absorption (XAS) and emission (XES) spectroscopy. We show, using reference compounds and ab initio calculations, that the presence of Pb?O and Sn?O interactions can be detected in the pre-edge region of the oxygen K-edge XAS. Via analysis of this interaction-sensitive pre-edge region, we find that Pb implantation results primarily in the clustering of Pb atoms. Conversely, with Sn implantation using identical conditions, strong Sn?O interactions are present, showing that Sn is coordinated with oxygen. The varying results between the two ion types are explained using both ballistic considerations and density functional theory calculations. We find that the substitution of Pb into Si sites in SiO<SUB>2</SUB> requires much more energy than substituting Sn in these same sites, primarily due to the larger size of the Pb ions. From these calculated formation energies it is evident that Pb requires far higher temperatures than Sn to be soluble in SiO<SUB>2</SUB>. These results help explain the complex processes which take place upon implantation and determine the final products.
Yun, Ji-Hye,Li, Xuanxuan,Park, Jae-Hyun,Wang, Yang,Ohki, Mio,Jin, Zeyu,Lee, Wonbin,Park, Sam-Yong,Hu, Hao,Li, Chufeng,Zatsepin, Nadia,Hunter, Mark S.,Sierra, Raymond G.,Koralek, Jake,Yoon, Chun Hong,C American Society for Biochemistry and Molecular Bi 2019 The Journal of biological chemistry Vol.294 No.3
<P>Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-<I>trans</I> retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.</P>