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Int. J. Mol. Sci., Volume 5, Issue 3 (March 2004), Pages 75-109

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Research

Open AccessArticle Theoretical Analysis of the Excited State Properties of Wybutine: A Natural Probe for Transfer RNA Dynamics
Int. J. Mol. Sci. 2004, 5(3), 75-83; doi:10.3390/i5030075
Received: 30 April 2003 / Accepted: 10 October 2003 / Published: 20 February 2004
Cited by 5 | PDF Full-text (129 KB)
Abstract
We have theoretically characterized the ground state and the excited state properties of wybutine, a naturally fluorescent modified base occuring in tRNAs, using configuration interaction singles (CIS) and time dependent density functional (TDDFT) methods. Both gas phase excited state properties and solvent effects,
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We have theoretically characterized the ground state and the excited state properties of wybutine, a naturally fluorescent modified base occuring in tRNAs, using configuration interaction singles (CIS) and time dependent density functional (TDDFT) methods. Both gas phase excited state properties and solvent effects, modelled through Onsager reaction field method, were considered. In addition to vertical excitation energies, the fluorescence transitions were calculated, based on S1 equilibrium geometry optimized at CIS level. Our computations show encouraging agreement with known experimental data either directly (TDDFT) or after applying empirical scaling (CIS). The fluorescence Stokes’ shift for the S0 Ã S1 transition is computed taking into account the contributions from both intramolecular and solvent reorganization processes. The results suggest that intramolecular relaxation of the S1 state accounts for the major part of the magnitude of the Stokes’ shift, while the role of solvent reorganization seems to be of less importance. Full article
Open AccessArticle NMR-based Structural Studies of the Glycosylated MUC1 Tandem Repeat Peptide
Int. J. Mol. Sci. 2004, 5(3), 84-92; doi:10.3390/i5030084
Received: 1 May 2003 / Accepted: 18 November 2003 / Published: 20 February 2004
PDF Full-text (314 KB) | HTML Full-text | XML Full-text
Abstract
MUC1 is a glycoprotein that plays an important role in cancer pathogenesis. In order to study the effect of glycosylation on the conformational propensities of the tandem repeat domain of MUC1, we have determined the structure of the MUC1 tandem repeat peptide AHGVTSAPDTRPAPGSTAPP,
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MUC1 is a glycoprotein that plays an important role in cancer pathogenesis. In order to study the effect of glycosylation on the conformational propensities of the tandem repeat domain of MUC1, we have determined the structure of the MUC1 tandem repeat peptide AHGVTSAPDTRPAPGSTAPP, O-glycosylated with the trisaccharide (α-Glc-1,4-β-Glc-1,4-α-GalNAc-) at Thr5. This glycopeptide was synthesized to model a heavily Oglycosylated threonine residue in the tandem repeat domain. The NMR experiments used in this study included TOCSY, NOESY, ROESY, DQF-COSY, HSQC and 1D NMR. The peak volumes determined using the program SPARKY were converted into distance constraints using the program CALIBA. The programs FiSiNOE and HABAS were used to generate angle constraints. Using conformational restraints obtained from NMR, the program DYANA was used to determine the structures of the peptide. Finally, structural refinement was performed within the SYBYL software package using GLYCAM parameters and Kollman-all atom types. The presence of strong sequential αN connectivities suggested an extended conformation of the peptide backbone. Strong sequential αδ connectivities were indicative of a trans conformation of the Ala-Pro peptide bonds. In addition, presence of sequential NN connectivities in the peptide segments Gly3-Val4-Thr5-Ser6, Asp9-Thr10-Arg11 and Gly-Ser16 were indicative of twist-like conformations of the peptide backbone in these peptide segments. Full article
Open AccessArticle The Interpretation of the Short Range Disorder in the Fluorene-TCNE Crystal Structure
Int. J. Mol. Sci. 2004, 5(3), 93-100; doi:10.3390/i5030093
Received: 1 May 2003 / Accepted: 18 July 2003 / Published: 20 February 2004
Cited by 13 | PDF Full-text (163 KB) | HTML Full-text | XML Full-text
Abstract
The interpretation of the short-range static and/or dynamic disorder in a crystal structure from X-ray data is often a rather complex problem. Recently, we synthesized and characterized three co-crystalline complexes between fluorene, showing C2v symmetry, and three electron withdrawing D2h compounds,
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The interpretation of the short-range static and/or dynamic disorder in a crystal structure from X-ray data is often a rather complex problem. Recently, we synthesized and characterized three co-crystalline complexes between fluorene, showing C2v symmetry, and three electron withdrawing D2h compounds, employing FTIR and Raman spectroscopy and single crystal X-ray diffraction techniques. The crystal structures of the complexes of fluorene with the three different electron withdrawing molecules are disordered in the solid state and only approximate structures were obtained by refinement of the single crystal data. Indeed, the fluorene moiety presents a very irregular geometry, showing for example C-C bonds ranging from 1.25Å to 1.75Å. Graphical inspection of the solved crystal structures indicates that the fluorene molecules in these co-crystalline complexes can assume two possible positions, both with 50% population. A two-step procedure to improve the disordered models is described. At first, the two possible ordered structures, with the fluorene molecule in only one of the two populated positions, are "separated" by molecular graphic techniques and then their geometry is fully optimized employing the periodic ab initio “CRYSTAL” code to obtain a chemically sensible model with reasonable distances and angles. The main aim of this communication is to demonstrate that ordered models can be obtained, starting from a disordered crystal structure, focusing our attention on the fluorene-TCNE molecular complex. Full article
Open AccessArticle A GMDH Approach to Modelling Gibbsite Solubility in Bayer Process Liquors
Int. J. Mol. Sci. 2004, 5(3), 101-109; doi:10.3390/i5030101
Received: 4 May 2003 / Accepted: 19 August 2003 / Published: 20 February 2004
Cited by 2 | PDF Full-text (154 KB) | HTML Full-text | XML Full-text
Abstract
The most widely employed industrial process for producing alumina (Bayer process) involves the dissolution of available aluminium hydroxide minerals present in raw bauxite into high temperature sodium hydroxide solutions. On cooling of the solution, or liquor in the industrial vernacular, Al is precipitated
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The most widely employed industrial process for producing alumina (Bayer process) involves the dissolution of available aluminium hydroxide minerals present in raw bauxite into high temperature sodium hydroxide solutions. On cooling of the solution, or liquor in the industrial vernacular, Al is precipitated from solution in the form of gibbsite (Al(OH)3). In order to optimise the process, a detailed knowledge of factors influencing gibbsite solubility is required, a problem that is confounded by the presence of liquor impurities. In this paper, the use of the Group Method of Data Handling (GMDH) polynomial neural network for developing a gibbsite equilibrium solubility model for Bayer process liquors is discussed. The resulting predictive model appears to correctly incorporate the effects of liquor impurities and is found to offer a level of performance comparable to the most sophisticated phenomenological model presented to date. Full article

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