Chemistry & Biochemistry

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    Structure of an eight-membered CN4S3 ring with the shortest known transannual s...s contact
    (International Union of Crystallography, 1985) Boeré, René T.; Oakley, Richard T.; Cordes, A. Wallace
    7-tert-Butyl-3-chloro- 1,3,5,2,4,6,8-trithiatetrazocine, CsH9C1N4S 3, Mr= 256"8, tetragonal, P42/n, a = 17.856 (2), c = 6.646 (1) A, V = 2118.9 (8)/k 3, z=8, Dx= 1.61gcm -3, 2(MoKa)=0.71073A, # =8.9cm -1, F(000)=1056, T=294K, final R= 0.049 for 1201 reflections. The molecule has a folded butterfly structure, with almost planar SNCNS and SNSNS fragments, and the C1 atom is endo. The transannular S-S contact is 2.378 (2)A, the shortest such distance in any thiazyl compound.
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    Structure of a bicyclic sulfur-nitrogen-carbon heterocyclic molecule
    (International Union of Crystallography, 1985) Cordes, A. Wallace; Oakley, Richard T.; Boeré, René T.
    7-Phenyl- 124324b'2,524-trithia-2,4,6,8,9-penta - azabicyclo[3.3.1]nonane, CTHsNsS 3, M r = 255.3, monoclinic, P2Jn, a = 5.958 (1), b = 22.954 (2), c= 7.428 (1) A,/I= 106.25 (1) °, V= 975.2 (4) A 3, Z=4, D x = 1.74 g cm -3, 2(Mo K~) = 0.71073 A, /~ = 7.00 cm -l, F(000) = 520, T = 293 K, R = 0.030 for 1363 unique observed reflections. The planar SNCNS and SNSNS components of the bicyclic molecule make dihedral angles of 137.1 and 118.3 ° with the SNS bridging unit. The S-N bonds connecting the NSN fragment to the CN3S 2 ring are much longer (1.728 A) than those in the remainder of the molecule (1.546- 1.630 A).
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    Structure of 1,3-dichloro-5-phenyl-1λ4,3λ4,2,4,6-dithiatriazine
    (International Union of Crystallography, 1985) Graham, J. B.; Cordes, A. W.; Oakley, Richard T.; Boeré, René T.
    C7HsC12N3S2, Mr=266.17, triclinic, P], a=6-028(1), b=9-985(2), c=10.157 (3) /~, ct= 117.33 (2), fl= 106.73(2), y=90.31(1) °, V= 513-3(4)/~3, Z=2, D x=1.72gcm -3, 2(MoK~t)= 0.71073 A, /1 = 9.85 cm -1, F(000) = 268, T= 293 K, R = 0.032 for 1547 unique observed reflections. The SNCNS portion of the ring is planar within 0-060 (2)/~ and the third N is displaced 0.336 (2) A from this plane on the side opposite the S-bonded C1 atoms. The S-N distances range from 1.581 (1) to 1.615 (2)/~ and the N-C distances are 1.327 (2) and 1.344 (2) ./k.
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    Structure of an eight-membered CN4S3 ring with a Ph3P=N substituent
    (International Union of Crystallography, 1986) Boeré, René T.; Ferguson, George; Oakley, Richard T.
    7-Phenyl-3-(triphenylphosphinimino)- 1,3,5,- 2,4,6,8-trithiatetrazocine, C25H20N5PS3, Mr = 517.64, monoclinic, P21/c, a = 13.957 (3), b = 9.242 (3), c = 19.473 (4)/k, fl= 102.80 (2) °, V= 2449.4 A 3, Z =4, Dx=l.4Ogcm -3, 2(MoKc0=0.71069A, ~= 3.8cm -1, F(000)=1072, T=293(1) K, final R= 0.038 for 2430 observed reflections. The molecule has a phenyl ring substituted at a planar carbon, and a PhaP=N group substituted at S in the 3-position. The CN4S3 ring is folded by 114.5 °, with an almost planar SNCNS fragment, and an endo-S-envelope SNSNS fragment (dihedral 145.0°). The PhaP=N substituent at S is endo and the transannular S...S contact is 2.415 (1)A.
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    The structure of the norbornadiene adduct of 5-phenyl-1,3,2,4,6-dithiatriazine
    (International Union of Crystallography, 1986) Cordes, A. Wallace; Craig, S. L.; Privett, J. A. James; Oakley, Richard T.; Boeré, René T.
    10-Phenyl- 1,8-dithia-9,11,12-triazatetracyclo- [6.3.1.1 a,6.02,7]tfideca- 1 (11),4,9,8 (12)-tetraene, C ~4- H13N3S2, Mr-- 287.4, monoclinic, P2 l, a = 5-789 (2), b=10.064(1), c--11.109(2)A, fl=94.78(2) °, V = 644.9 (4)/~3, Z = 2, D x = 1.48 g cm -3, 2(Mo Kct) =0.71073/~, p-- 3.84cm -~, F(000)= 300, T-- 293 K, R -- 0.037 for 1203 unique observed reflections. The norbornadiene bonds to the sulfur atoms in the exo-fl orientation and the nitrogen atom between the sulfur atoms is displaced 0.802 (4)/~ from the SNCNS plane. The C-N bond lengths are equal [1.335 (5)A] and the S--N bond lengths in a very narrow range of values [1.637 (4)-1.652 (4) A].
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    Exchange holes in inhomogeneous systems: a coordinate-space model
    (American Physical Society, 1989) Becke, A. D.; Roussel, Marc R.
    We present a new coordinate-space model of spherically averaged exchange-hole functions in inhomogeneous systems that depends on local values of the density and its gradient and Laplacian, and also the kinetic energy density. Our model is completely nonempirical, incorporates the uniform-density electron gas and hydrogenic atom limits, and yields the proper 1lr asymptotic exchange potential in finite systems. Comparisons of model exchange energies, holes, and potentials with exact Hartree-Fock results in selected atoms are very encouraging.
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    3,7-Di-tert-butyl-1,5,2,4,6,8-dithiatetrazocine
    (International Union of Crystallography, 1995) Parvez, Masood; Boeré, René T.; Derrick, Sean; Moock, Klaus H.
    The eight-membered ring in the title compound, C10HI8N4S2, lies about an inversion centre and is essentially planar with normal bond lengths and angles [mean C--S 1.569 (2) and mean C--N 1.326 (3)A].
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    A dimer of 4-(4-methoxyphenyl)-1,2,3,5-diselenadiazole
    (International Union of Crystallography, 1995) Parvez, Masood; Boeré, René T.; Moock, Klaus H.
    The analysis of the title compound, C8H7N2OSe2, shows that its crystals are composed of weakly linked dimers, with intramolecular Se--Se distances of 2.343(3) and 2.345 (2)A,, intermolecular Se-.-Se distances of 3.193(3) and 3.316 (3) /k, and lateral Se...Se interactions of 3.514 (2) and 3.579 (3) A,.
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    Infrared diode laser spectroscopy of the CCO radical: the 2v1-v1 and v1+v3-v3 difference bands
    (AIP Publishing, 1998) Moazzen-Ahmadi, N.; Boeré, René T.
    The 2n 12n 1 and n 11n 32n 3 difference bands of the CCO radical in the gas phase have been studied using a tunable infrared diode laser spectrometer. The CCO radical was produced using a flowing mixture of carbon suboxide and helium subjected to a hollow-cathode discharge. The spectral region between 1920– 1960 cm21 was probed. Ninety and seventy-five rovibrational transitions were measured in the 2n 12n 1 and n 11n 32n 3 bands, respectively. The analyses of these bands yielded spectroscopic constants for the ~001!, ~200!, and ~101! vibrational states. The band origins for 2n 12n 1 and n 11n 32n 3 were determined to be 1941.85761(54) cm21 and 1936.79402(56) cm21, respectively.
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    Equilibrium configuration of systems of trapped ions
    (American Physical Society, 1999) Beekman, Richard A.; Roussel, Marc R.; Wilson, P. J.
    We have computed the equilibrium conformations of clusters of up to 100 ions in a spherically symmetric harmonic trap by a simple optimization strategy called seeding in which ions are added or removed from previously discovered minima. In each case, we have found at least as good a minimum as was previously known and believe that we have located the global minimum. We have additionally located a number of local minima and some saddle points. A balancing condition between the Coulomb and trapping terms which all of the critical points of the potential energy surface must satisfy was used to estimate the errors in the computed energies.
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    Preparation and x-ray structure of 4-N,N'-bis(trimethylsilyl)- amino-3,5-diisopropylphenylselenium trichloride
    (Verlag der Zeitschrift für Naturforschung, 1999) Maaninen, Arto; Boeré, René T.; Chivers, Tristram; Parvez, Masood
    The reaction of SeCU or SeCF with /V,/V’-bis(trimethylsilyl)-2,6-diisopropylaniline occurs not at the nitrogen atom but by electrophilic aromatic substitution at C-4 of the phenyl ring to give [(CH3)3Si]2NC6H2('Pr:)SeCl3, which crystallizes as the chloro-bridged dimer in the triclinic system, space group Pi, a - 10.2598(17), b = 13.665(3), c = 9.7838(10) A, a = 90.056(13), ß = 102.439(11), 7 = 70.922(14)°, V = 1262.3(4) A \Z = 1. The dimer contains an essentially planar CUSe^-Cl^SeCU unit, with trans apical (Me3SihNC6H2('Pr)2 groups, resulting in approximately square pyramidal geometry at Se. The bridging Se-Cl distances are unequal at 2.587(2) and 2.749(2) A.
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    Coordinate files for the equilibrium geometries of ions in an isotropic trap
    (1999) Beekman, Richard A.; Roussel, Marc R.; Wilson, P. J.
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    Synchronization by irregular inactivation
    (American Physical Society, 2000) Closson, Taunia L. L.; Roussel, Marc R.
    Many natural and technological systems have on/off switches. For instance, mitosis can be halted by biochemical switches which act through the phosphorylation state of a complex called mitosis promoting factor. If switching between the on and off states is periodic, chaos is observed over a substantial portion of the on/off time parameter plane. However, we have discovered that the chaotic state is fragile with respect to random fluctuations in the on time. In the presence of such fluctuations, two uncoupled copies of the system (e.g., two cells) controlled by the same switch rapidly synchronize.
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    Electrochemistry of redox-active Group 15/16 heterocycles
    (Elsevier, 2000) Boeré, René T.; Roemmele, Tracey L.
    This review is a critical overview of the literature on electrochemistry of unsaturated ring compounds containing bonds between Group 15 and Group 16 elements (principally S and N), including metallacycles. It contains a detailed compilation of measured redox potentials and the conditions under which these were obtained for over 200 compounds. An introduction to the application of solution electrochemistry to this class of compounds is provided, and the relevance of such measurements to materials design is discussed.
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    Transition from self-replicating behavior to stationary patterns induced by concentration-dependent diffusivities
    (American Physical Society, 2001) Roussel, Marc R.; Wang, Jichang
    In this Letter, we report the observation of a transition from self-replicating behavior to stationary spatial structures induced by concentration-dependent diffusivities in the excitable Gray-Scott medium. Notably, the transition occurs even though there is no change in the relative diffusivities between the activator and the inhibitor. In contrast to the well-known Turing patterns, the obtained time-independent spatial structure has no intrinsic wavelength and the asymptotic state depends exclusively on the initial perturbations. This study illustrates that variable diffusivities can also have profound effects on pattern formation and selection in excitable media.
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    Code and examples for C++ object-oriented differential equation integrators
    (2003) Roussel, Catharine J.; Roussel, Marc R.
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    The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome
    (Cold Springs Harbor Laboratory Press, 2003) Gu, Shan-Qing; Peske, Frank; Wieden, Hans-Joachim; Rodnina, Marina V.; Wintermeyer, Wolfgang
    The signal recognition particle (SRP) from Escherichia coli, composed of Ffh protein and 4.5S RNA, mediates membrane targeting of translating ribosomes displaying a signal or signal-anchor sequence. SRP binds at the peptide exit of the large ribosomal subunit. Structural details of the interaction are not known. Here, the position of Ffh or SRP on the ribosome was probed by using site-specific UV-induced crosslinking by p-azidophenacyl bromide (AzP) attached to a number of cysteine residues engineered into surface positions of Ffh. Efficient crosslinking to vacant ribosomes took place from two positions (AzP17 and AzP25) in the N domain of Ffh, both with Ffh and SRP. Both AzP17 and AzP25 were predominantly crosslinked to ribosomal protein L23 that is located at the peptide exit of the 50S subunit.The SRP receptor, FtsY, did not change the crosslink pattern, whereas the presence of a nascent signal peptide on the ribosome resulted in a second crosslink between Ffh(AzP17) and protein L23, indicating that binding to the nascent signal peptide induced a slightly different arrangement of SRP on the ribosome. These results indicate a model of the topographical arrangement of SRP at the peptide exit of the 50S ribosomal subunit.
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    De novo cytosine methylation in the differentiating macronucleus of the stichotrichous ciliate Stylonychia lemnae
    (Oxford University Press, 2003) Juranek, Stefan; Wieden, Hans-Joachim; Lipps, Hans J.
    Dramatic DNA reorganization and elimination processes occur during macronuclear differentiation in ciliates. In this study we analyzed whether cytosine methylation of specific sequences plays a functional role during DNA rearrangement. Three classes of sequences, macronuclear-destined sequences (MDSs, pCE7), members from a large family of transposon-like elements and micronuclear-specific sequences (pLJ01), differing in their structure and future destiny during nuclear differentiation, were studied in the micronucleus, the developing macronucleus and, when present, in the mature macronucleus. While the MDSs become processed to a 1.1 and 1.3 kb gene-sized macronuclear DNA molecule, the family of transposon-like elements represented by MaA81 becomes removed late in the course of polytene chromosome formation. The micronuclear-specific sequence pLJ01 is eliminated together with bulk micronuclear DNA during degradation of polytene chromosomes. No methylated cytosine could be detected in the vegetative macronucleus and no difference in methylation pattern was observed either between micronucleus and developing macronucleus in MDSs or in a micronuclear-speci®c sequence. However, a significant percentage of the cytosines contained in the transposon-like element becomes methylated de novo in the course of macronuclear differentiation. This is the first demonstration that cytosine methylation in speci®c sequences occurs during macronuclear differentiation and may provide a first step towards understanding epigenetic factors involved in DNA processing
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    The diversity of the stable and persistent phosphorus-containing radicals
    (American Chemical Society, 2005) Armstrong, A.; Chivers, T.; Boeré, René T.
    Stable and persistent phosphorus-containing radicals can be divided into five general categories: phosphinyl, diphosphanyl, 1,3-diphosphaallyl, lithiated tetrakisimidophosphates, and phosphaverdazyl systems. The syntheses, structures, EPR spectroscopic characterization, and sources of stability of these neutral radicals are presented and compared.
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    Synthesis, crystal structure and DFT calculations on 2,6-diisopropylphenylcopper: its use in the preparation of dichloro-2,6-diisopropylphenylphosphine
    (Elsevier, 2006) Boeré, René T.; Masuda, Jason D.; Tran, Peter
    The homoleptic aryl copper reagent [Cu4Dipp4] (Dipp = 2,6-diisopropylphenyl) has been prepared and structurally characterized by a single-crystal X-ray diffraction study. Its tetrameric structure differs in significant details from that of the previously reported [Cu4Tripp4] (Tripp = 2,4,6-triisopropylphenyl). The electronic structure of the cluster has been probed through B3LYP/6-3111G(2d,p)//B3LYP/6-31G calculations on [Cu4Ph4] constrained to D2d symmetry. The utility of the new copper reagent is demonstrated by the preparation of pure DippPCl2, for which the crystal structure is also reported.