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Synthesis and characterization of 2-chloro-3-benzylthiopyrrolo[1,2-a]- benzimidazol-1-one and 2,3-di(benzylthio)pyrrolo[1,2-a]benzimidazol-1-one.

Description: The reaction between o-phenylenediamine and 2,3-dichloromaleic anhydride has been probed and found to give 2,3-dichloropyrrolo[1,2-a]- benzimidazol-1-one as the major product. Chlorine substitution in 2,3-dichloropyrrolo[1,2-a]benzimidazol-1-one by added benzylthiol occurs in the presence of pyridine to provide the corresponding monosulfide and disulfide derivatives. The first benzylthiol ligand undergoes reaction at the C-3 position of the five-membered pyrrolo-1-one ring, with the addition of the second benzylthiol ligand occurring at the remaining chlorine-substituted carbon. The mono- and disulfide derivatives have been isolated and characterized in solution by NMR, IR, and UV-vis spectroscopies, and the solid-state structure of 2,3-di(benzylthio)pyrrolo[1,2-a]benzimidazol-1-one has been established by X-ray crystallography.
Date: December 2003
Creator: Huang, Shih-Huang
Partner: UNT Libraries

cctbx news

Description: The 'Computational Crystallography Toolbox' (cctbx, http://cctbx.sourceforge.net/) is the open-source component of the Phenix project (http://www.phenix-online.org/). Most recent cctbx developments are geared towards supporting new features of the phenix.refine application. Thus, the open-source mmtbx (macromolecular toolbox) module is currently being most rapidly developed. In this article we give an overview of some of the recent developments. However, the main theme of this article is the presentation of a light-weight example command-line application that was specifically developed for this newsletter: sequence alignment and superposition of two molecules read from files in PDB format. This involves parameter input based on the Phil module presented in Newsletter No. 5, fast reading of the PDB files with the new iotbx.pdb.input class, simple sequence alignment using the new mmtbx.alignment module, and use of the Kearsley (1989) superposition algorithm to find the least-squares solution for superposing C-alpha positions. The major steps are introduced individually, followed by a presentation of the complete application. The example application is deliberately limited in functionality to make it concise enough for this article. The main goal is to show how the open-source components are typically combined into an application. Even though the example is quite specific to macromolecular crystallography, we believe it will also be useful for a small-molecule audience interested in utilizing the large open-source library of general crystallographic algorithms (see our previous articles in this newsletter series) to build an application. We describe recent developments of the Computational Crystallography Toolbox.
Date: November 22, 2006
Creator: Grosse-Kunstleve, Ralf W.; Zwart, Peter H.; Afonine, Pavel V.; Ioerger, Thomas R. & Adams, Paul D.
Partner: UNT Libraries Government Documents Department

Space Groups and Lattice Complexes

Description: From Abstract: "The lattice complex is to the space group what the site is to the point group - an assemblage of symmetry-related equivalent points. The Tables list site sets and lattice complexes in standard and alternate representation. The higher the symmetry of the crystal structures is, the more useful the lattice-complex approach should be on the road to the ultimate goal their classification."
Date: May 1973
Creator: Fisher, Werner; Burzlaff, Hans; Hellner, Erwin & Hellner, Erwin
Partner: UNT Libraries Government Documents Department

Chlorido(4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine)platinum(II) chloride toluene monosolvate

Description: In the title compound, [PtCl(C₂₇H₃₅N₃)]Cl·C₇H₈, the Ptᴵᴵ atom is coordinated in a pseudo-square-planar fashion by the N atoms of a 4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine ligand and a Cl atom.
Date: November 22, 2010
Creator: Batrice, Rami J.; Nesterov, Vladimir N. & Smucker, Bradley W.
Partner: UNT College of Arts and Sciences


Description: The atomic positions of the Rh(111) + ({radical}3 x {radical}3)R30{sup o} CO and CO{sub 2} surfaces are analyzed by dynamical LEED. The Rh(111) + ({radical}3 x {radical}3)R30{sup o} CO and CO{sub 2} systems produce identical I-V curves, confirming the dissociation of CO{sub 2} to CO on this surface. The adsorbed CO is found to stand perpendicular to the surface with the carbon end down at an atop site (that is, terminally bonded). The CO overlayer spacings are d{sub RhC} = 1.95 {+-} 0.1 {angstrom} and d{sub CD} = 1.07 {+-} 0.1 {angstrom}. This geometry yields a Zanazzi-Jona R-factor of 0.40 and a Pendry R-factor of 0.50.
Date: September 1, 1980
Creator: Koestner, R.J.; Van Hove, M.A. & Somorjai, G.A.
Partner: UNT Libraries Government Documents Department

John Pendry: His Contributions to the Development of LEED Surface Crystallography

Description: In this paper we discuss the pivotal role played by Sir John Pendry in the development of Low Energy Electron Diffraction (LEED) during the past three decades; the earliest understanding on the physics of LEED to the development of sophisticated methods for the structural solution of complex surfaces.
Date: October 15, 2007
Creator: Somorjai, Gabor A. & Rous, P. J.
Partner: UNT Libraries Government Documents Department

Structure of the LDL receptor extracellular domain at endosomalpH

Description: The structure of the low-density lipoprotein receptor extracellular portion has been determined. The document proposes a mechanism for the release of lipoprotein in the endosome. Without this release, the mechanism of receptor recycling cannot function.
Date: September 5, 2002
Creator: Rudenko, Gabby; Henry, Lisa; Henderson, Keith; Ichtchenko,Konstantin; Brown, Michael S.; Goldstein, Joseph L. et al.
Partner: UNT Libraries Government Documents Department

The Crystal Cavities of the New Jersey Zeolite Region

Description: From abstract: The crystal cavities present in the mineral complex of the New Jersey traprock region have long excited the interest of mineralogists. In 1914 Fenner made the first detailed and comprehensive study of these cavities and suggested that babingtonite was the original mineral. Soon after this anhydrite was found occupying parts of some of the cavities at one of the quarries. At this time, too, Wherry concluded that glauberite was the original mineral of some of the cavities because of his studies of similar crystal cavities in Triassic shale at different places.
Date: 1932
Creator: Schaller, Waldemar T.
Partner: UNT Libraries Government Documents Department

Connecting the micro to the mesoscale: review and specific examples

Description: Historically, dislocation are thought of and treated as dual objects. The large lattice distortions inside the core region warrant an atomistic treatment, whereas the slightly distorted crystal outside of the core is well represented within a linear elastic framework. Continuum dislocation theory is powerful and elegant. Yet, it is unable to fully account for the structural differentiation of dislocation behavior, say, within the same crystallography class. The source of these structural variations is mostly in the dislocation core (see [1] for an excellent review). In the past several years, the gap between the two approaches (atomistic and continuum-mesoscopic) for modeling dislocation behavior has started to close, owing to the overlap of the time and length scales accessible to them [2]. The current trend in dislocation modeling is to try to abstract the local rules of dislocation behavior, including their mobility and interactions, from the atomistic simulations and then incorporate these rules in a properly defined continuum approach, e.g. Dislocation Dynamics. The hope is that, by combining the two descriptions, a truly predictive computational framework can be obtained. For this emerging partnership to develop, some interesting issues need to be resolved concerning both physics and computations. It is from this angle that I will try to discuss several recent developments in atomistic simulations that may have serious implications for connecting atomistic and mesoscopic descriptions of dislocations. These are intended to support my speculations on what can and should be expected from atomistic calculations in the near future, for further development of dislocation theory of crystal plasticity.
Date: August 26, 1999
Creator: Bulatov, V
Partner: UNT Libraries Government Documents Department

Titanium Boride Formation and Its Subsequent Influence on Morphology and Crystallography of Alpha Precipitates in Titanium Alloys

Description: Over the last two decades there has been an increased interest in understanding the influence of trace boron additions in Ti alloys. These additions refine the prior β grain size in as-cast Ti alloys along with increasing their modulus and yield strength due to the precipitation of TiB. TiB also acts as a heterogeneous nucleation site for α precipitation and has been shown to influence the α phase morphology. B is completely soluble in liquid Ti but has a negligible solubility in both body centered cubic β and hexagonal close packed α phases of Ti. Thus, during solidification of hypoeutectic B containing alloys, B is rejected from β into the liquid where it reacts with Ti to form pristine single crystal whiskers of TiB. Despite a substantial amount of reported experimental work on the characterization of TiB precipitates, its formation mechanism and influence on α phase precipitation are still not clear. The current work is divided into two parts – (i) understanding the mechanism of TiB formation using first principles based density functional theory (DFT) calculations and (ii) elucidating how TiB influences the α phase morphology and crystallography in titanium alloys using electron microscopy techniques. TiB exhibits anisotropic growth morphology with [010] direction as its predominant growth direction and displays a hexagonal cross section with (100), (101), and (10) as the bounding planes. A high density of stacking faults has been experimentally observed on the (100) plane. The present study, by using DFT based nudged elastic band (NEB) calculations, elucidates for the first time that the diffusion of B through TiB is via an interstitial-assisted mechanism as opposed to vacancy-assisted mechanism hypothesized in literature. This one dimensional interstitial-assisted diffusion results in the anisotropic growth of TiB. In addition, the energetics of TiB- α interfaces was calculated to understand the hexagonal ...
Date: December 2013
Creator: Nandwana, Peeyush
Partner: UNT Libraries

Crystallographic Topology 2: Overview and Work in Progress

Description: This overview describes an application of contemporary geometric topology and stochastic process concepts to structural crystallography. In this application, crystallographic groups become orbifolds, crystal structures become Morse functions on orbifolds, and vibrating atoms in a crystal become vector valued Gaussian measures with the Radon-Nikodym property. Intended crystallographic benefits include new methods for visualization of space groups and crystal structures, analysis of the thermal motion patterns seen in ORTEP drawings, and a classification scheme for crystal structures based on their Heegaard splitting properties.
Date: August 1, 1999
Creator: Johnson, C.K.
Partner: UNT Libraries Government Documents Department


Description: Informal reports are presented on experimental nuclear physics, mass spectroscopy, and crystallography. Each individual project reports about once in 3 months. Those not reported in a particular issue are listed separately in the table of contents with a reference to the last issue in which each appeared. (For preceding period see ANL6164.) (W.D.M.)
Date: October 31, 1960
Partner: UNT Libraries Government Documents Department

Beta-Phosphinoethylboranes as Ambiphilic Ligands in Nickel-Methyl Complexes

Description: The ambiphilic {beta}-phosphinoethylboranes Ph{sub 2}PCH{sub 2}CH{sub 2}BR{sub 2} (BR{sub 2} = BCy{sub 2} (1a), BBN (1b)), which feature a ethano spacer CH{sub 2}CH{sub 2} between the Lewis acidic boryl and Lewis basic phosphino groups, were synthesized in nearly quantitative yields via the hydroboration of vinyldiphenylphosphine. Compounds 1a and 1b were fully characterized by elemental analysis, and by NMR and IR spectroscopy. X-ray crystallographic studies of compound 1b revealed infinite helical chains of the molecules connected through P{hor_ellipsis}B donor-acceptor interactions. The ability of these ambiphilic ligands to concurrently act as donors and acceptors was highlighted by their reactions with (dmpe)NiMe{sub 2}. Zwitterionic complexes (dmpe)NiMe(Ph{sub 2}PCH{sub 2}CH{sub 2}BCy{sub 2}Me) (2a) and (dmpe)NiMe(Ph{sub 2}PCH{sub 2}CH{sub 2}[BBN]Me) (2b) were generated via the abstraction of one of the methyl groups, forming a borate, and intramolecular coordination of the phosphine moiety to the resulting cationic metal center. Compound 2b was characterized by X-ray crystallography. Furthermore, B(C{sub 6}F{sub 5}){sub 3} abstracts the methyl group of a coordinated borate ligand to generate a free, 3-coordinate borane center in [(dmpe)NiMe(1a)]{sup +}[MeB(C{sub 6}F{sub 5}){sub 3}]{sup -} (3).
Date: October 28, 2007
Creator: Fischbach, Andreas; Bazinet, Patrick R.; Waterman, Rory & Tilley, T. Don
Partner: UNT Libraries Government Documents Department

A Variation of the F-Test for Determining Statistical Relevance ofParticular Parameters in EXAFS Fits

Description: A general problem when fitting EXAFS data is determining whether particular parameters are statistically significant. The F-test is an excellent way of determining relevancy in EXAFS because it only relies on the ratio of the fit residual of two possible models, and therefore the data errors approximately cancel. Although this test is widely used in crystallography (there, it is often called a 'Hamilton test') and has been properly applied to EXAFS data in the past, it is very rarely applied in EXAFS analysis. We have implemented a variation of the F-test adapted for EXAFS data analysis in the RSXAP analysis package, and demonstrate its applicability with a few examples, including determining whether a particular scattering shell is warranted, and differentiating between two possible species or two possible structures in a given shell.
Date: July 25, 2006
Creator: Downward, L.; Booth, C.H.; Lukens, W.W. & Bridges, F.
Partner: UNT Libraries Government Documents Department