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Different Charge States (different + charge_states)
Selected AbstractsDensity functional study of the heme moiety of cytochrome c,,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Anil Kumar Abstract A model of cytochrome c (Cyt-c) including the porphyrin ring, a methionine residue (Met), and the imidazole ring of histidine (His), the latter two being situated above and below the iron (Fe) atom of the porphyrin ring, was studied using Density Functional Theory (DFT). The geometries of the model Cyt-c complex with the Fe atom in two different charge states were fully optimized, i.e., in singlet and triplet states for Fe and in doublet and quartet states for Fe3+. The B3LYP method of DFT along with the 3-21G* basis set for C, H, N, and O atoms and the Lanl2dz basis set for the Fe atom was used. We found that with Fe3+, the doublet spin state is the ground state and the quartet state lies slightly above it. The geometry of the singlet spin state is similar to that of the doublet and quartet states. However, methionine has different conformations when Fe has zero charge (singlet, triplet states) relative to the situation when Fe has +3 charges (doublet, quartet states). The Met chain is folded instead of remaining extended in going from the singlet or triplet spin state to the doublet or quartet state and the folding is stabilized by an intramolecular CH..O hydrogen bond. The optimized geometrical parameters of the model of Cyt-c are usually in satisfactory agreement with those observed experimentally. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Ingredients Necessary for Proton Transfer in EnzymesISRAEL JOURNAL OF CHEMISTRY, Issue 2 2009Steve Scheiner The transfer of a proton across a hydrogen bond can be influenced by a number of factors, including H-bond length, intramolecular angles, and the presence of neighboring groups. The ability of different factors to push a proton across the H-bond is examined for a specific and very important pair of catalytic groups, Ser-195 and His-57, within the context of a serine proteinase enzyme. The influence of residue Asp-102 is considered for different charge states, as is the nature of the surrounding medium. Also examined are the perturbations introduced by the substrate and external ions and dipoles. [source] Inhomogeneous surface electronic properties and charge ordering in epitaxial Fe3O4 films on MgO(001)PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 12 2007A. Subagyo Abstract We report scanning tunneling microscopy (STM) study of surface electronic properties and charge ordering of epitaxially grown magnetite, Fe3O4, (001) films exhibiting high density of antiphase domain boundaries (APBs). STM measurements using a W tip reveal surface termination at B-sites. Fe ions with a 0.3 nm periodicity, i.e., a single atomic distance are observed. Current imaging tunneling spectroscopy reveals the alternation of two kinds of current peaks with a 0.6 nm periodicty indicating the presence of charge ordering consisted of Fe dimers with different charge states. STM measurements using a magnetic Ni tip provide higher contrast of the charge ordering. The APBs can modify the charge ordering as ordered and disordered areas are observed on adjacent domains separated by an APB. These strongly indicate that APBs can induce inhomogeneous properties on the surface of Fe3O4(001) films. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Modelling the light induced metastable effects in amorphous siliconPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 2 2008G. Munyeme Abstract We present results of computer simulations of the light induced degradation of amorphous silicon solar cells. It is now well established that when amorphous silicon is illuminated the density of dangling bond states increases. Dangling bond states produce amphoteric electronic mid-gap states which act as efficient charge trapping and recombination centres. The increase in dangling bond states causes a decrease in the performance of amorphous silicon solar cells. To show this effect, a modelling approach has been developed which uses the density of localised states with exponentially increasing band-tails and dangling bond defect states distribution chosen according to the defect pool model. The calculation of the evolution of dangling bond state density during illumination has been achieved through a dynamic scaling relation derived from a defect creation model. The approach considers the amphoteric nature of the dangling bond state and thus accounts for the contributions of the different charge states of the dangling bond during the degradation process. This paper attempts to describe the simulation approach which calculates the defect density as a function of energy, position in the solar cell and illumination time. In excellent agreement with other workers, our simulation results show that the increase in the density of neutral dangling bond states during illumination is higher than of the charged states. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A new strategy to filter out false positive identifications of peptides in SEQUEST database search resultsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2007Jiyang Zhang Abstract Based on the randomized database method and a linear discriminant function (LDF) model, a new strategy to filter out false positive matches in SEQUEST database search results is proposed. Given an experiment MS/MS dataset and a protein sequence database, a randomized database is constructed and merged with the original database. Then, all MS/MS spectra are searched against the combined database. For each expected false positive rate (FPR), LDFs are constructed for different charge states and used to filter out the false positive matches from the normal database. In order to investigate the error of FPR estimation, the new strategy was applied to a reference dataset. As a result, the estimated FPR was very close to the actual FPR. While applied to a human K562 cell line dataset, which is a complicated dataset from real sample, more matches could be confirmed than the traditional cutoff-based methods at the same estimated FPR. Also, though most of the results confirmed by the LDF model were consistent with those of PeptideProphet, the LDF model could still provide complementary information. These results indicate that the new method can reliably control the FPR of peptide identifications and is more sensitive than traditional cutoff-based methods. [source] On the use of ESI-QqTOF-MS/MS for the comparative sequencing of nucleic acidsBIOPOLYMERS, Issue 6 2009Herbert Oberacher Abstract The usability of a quadrupole,quadrupole,time-of-flight (QqTOF) instrument for the tandem mass spectrometric sequencing of oligodeoxynuleotides was investigated. The sample set consisted of 21 synthetic oligodeoxynucleotides ranging in length from 5 to 42 nucleotides. The sequences were randomly selected. For the majority of tested oligonucleotides, two or three different charge states were selected as precursor ions. Each precursor ion was fragmented applying several different collision voltages. Overall 282 fragment ion mass spectra were acquired. Computer-aided interpretation of fragment ion mass spectra was accomplished with a recently introduced comparative sequencing algorithm (COMPAS). The applied version of COMPAS was specifically optimized for the interpretation of information-rich spectra obtained on the QqTOF. Sequences of oligodeoxynucleotides as large as 26-mers were correctly verified in >94% of cases (182 of 192 spectra acquired). Fragment ion mass spectra of larger oligonucleotides were not specific enough for sequencing. Because of the occurrence of extensive internal fragmentation causing low sequence coverage paired with a high probability of assigning fragment ions to wrong sequences, tandem mass spectra obtained from oligonucleotides consisting of 30 and more nucleotides could not be used for sequence verification neither manually nor with COMPAS. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 401,409, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell-Wall Analogue Peptides: Experimental and Theoretical StudiesCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2009Zhibo Yang Dr. Abstract Charge matters! The charge state significantly influences the conformation and the binding energy between vancomycin antibiotic and bacterial cell-wall analogue peptides (see figure). Surface-induced dissociation (SID) studies provide a quantitative comparison between the stabilities of different charge states of the complex. In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the noncovalent complex between the vancomycin and the cell-wall peptide analogue N,,N, -diacetyl- L -Lys- D -Ala- D -Ala (V,Ac2LKdAdA). The binding energies between the vancomycin and the peptide were obtained from the RRKM (Rice, Ramsperger, Kassel, Marcus) modeling of the time- and energy-resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex towards fragmentation increases in the order: doubly protonated
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