			Home About us Contact

Dissociation Pathways (dissociation + pathway)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Electrospray tandem mass spectrometry of alkali-cationized BocN-carbo- ,,, - and - ,,, -peptides: differentiation of positional isomers,

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2006
P. Nagi Reddy
Dissociation pathways of a series of alkali-cationized hybrid peptides, viz., Boc- ,,, - and - ,,, -carbopeptides, synthesized from C-linked carbo- ,3 -amino acids [Caa (S)] and , -alanine (L-Ala), have been investigated by electrospray ionization tandem mass spectrometry. The positional isomers (six pairs) of the cationized ,,, - and ,,, -peptides can be differentiated by the collision-induced dissociation (CID) spectra of their [M,+,Cat-Boc,+,H]+ ions which give characteristic series of alkali-cationized C- (x, y, z) and N-terminal (a, b, c) ions. Another noteworthy difference is cationized ,,, -peptides eliminate a molecule of ammonia whereas this pathway is absent for ,,, -peptides. This is useful for identifying the presence of a , -amino acid at the N-terminus. The CID spectra of [M,+,Cat-Boc,+,H]+ ions of these peptide acids show abundant rearrangement [bn,+,17,+,Cat]+ (n,=,1 to n,1) ions which is diagnostic for distinguishing between , - and , -amino acid at the C-terminus. MSn experiments of [bn,+,Li,H]+ ions from these hybrid peptides showed the loss of CO and 72 u giving rise to [an,+,Li,H]+ and cationized nitrile product ions which render support to earlier proposals that b or [bn,+,Cat,H]+ ions have protonated or cationized oxazolinone structures, respectively. Copyright © 2006 John Wiley & Sons, Ltd. [source]

Ligand Association/Dissociation Paths and Ill-Defined Coordination Numbers

CHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2010
Antonio Ruiz-Martínez
Abstract The continuous shape measures approach provides a means for handling the common situation in which a metal atom presents an ill-defined coordination number. Those cases are characterized by the presence of secondary interactions to Lewis bases at distances significantly longer than those expected for a chemical bond. Systematic ways of analyzing ligand association/dissociation pathways that describe such structures and their application to a variety of specific cases are presented. The concepts and methodology presented here apply to molecules and extended solids as well and provide, when needed, a more flexible and precise stereochemical description of the metal coordination sphere than that of an integer coordination number and the associated polyhedral shape. El mètode de les mesures contínues de forma ens permet tractar la situació trobada freqüentment, en què un àtom metàl,lic presenta un nombre de coordinació no ben definit, caracteritzat per la presència d,interaccions secundàries amb bases de Lewis a distàncies significativament més llargues que les que correspondrien a un enllaç químic. Aquí es presenten formes sistemàtiques d,analitzar els camins d,associació/dissociació de lligands que descriuen aquestes estructures, així com llur aplicació a diverses famílies de compostos. Els conceptes i la metodologia presentats en aquest article s'apliquen tant a molècules com a sòlids infinits i ens proporcionen una descripció estereoquímica més flexible i alhora precisa de les esferes de coordinació que no pas un nombre de coordinació enter i la forma polièdrica associada. [source]

The formation of neutral CCCO2H and HCCCO2 molecules from anionic precursors in the gas phase: a joint experimental and theoretical study

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 24 2005
Mark Fitzgerald
Calculations at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31G(d) level of theory indicate that the anions ,CCCO2H and HCCCO are stable species in their singlet states. Upon collision-induced, vertical one-electron oxidation under neutralisation-reionisation (,NR+) conditions, they produce the neutral molecules CCCO2H and HCCCO2, respectively. Some of the CCCO2H neutrals should be stable for the duration of the neutralisation-reionisation experiment (10,6,s), while others will dissociate to CCCO and OH (requires 125,kJ,mol,1). In contrast, neutral HCCCO2 is expected to be much less stable, and dissociate to HCC and CO2 (37,kJ,mol,1). Neither CCCO2H nor HCCCO2 is expected to interconvert, or to rearrange to other isomers. The anions ,CCCO2H and HCCCO have been formed in the ion source of the mass spectrometer by the reactions between (CH3)3SiCCCO2H and F, and HCCCO2Si(CH3)3 and F,, respectively. The ,NR+ spectrum of ,CCCO2H shows a recovery signal and also indicates that the lowest energy dissociation pathway of neutral CCCO2H corresponds to the loss of OH. The ,NR+ spectrum of HCCCO2 displays little or no recovery signal, and the spectrum is dominated by the [CO2]+ ion. The experimental observations are in agreement with the predictions of the extensive theoretical studies. Copyright © 2005 John Wiley & Sons, Ltd. [source]

Infrared Multiple-Photon Dissociation Mechanisms of Peptides of Glycine

CHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2008
Ronghu Wu Dr.
Peptide patterns: The current experimental results indicate that infrared multiple-photon dissociation (IRMPD) of peptides forms more structurally informative sequence b and y ions, and fewer less useful nonsequence ions. Also the dissociation pathways are the same through excitation of different modes of the peptide. For the first time, it has been confirmed that the peptide dissociation pathway is not related to the initial protonation site or the conformation (e.g., cyclic or linear, see graphic) of the peptide. [source]

Screening for the calstabin-ryanodine receptor complex stabilizers JTV-519 and S-107 in doping control analysis

DRUG TESTING AND ANALYSIS, Issue 1 2009
Mario Thevis
Abstract Recent studies outlined the influence of exercise on the stability of the skeletal muscle calstabin1-ryanodine receptor1-complex, which represents a major Ca2+ release channel. The progressive modification of the type-1 skeletal muscle ryanodine receptor (RyR1) combined with reduced levels of calstabin1 and phosphodiesterase PDE4D3 resulted in a Ca2+ leak that has been a suggested cause of muscle damage and impaired exercise capacity. The use of 1,4-benzothiazepine derivatives such as the drug candidates JTV-519 and S-107 enhanced rebinding of calstabin1 to RyR1 and resulted in significantly improved skeletal muscle function and exercise performance in rodents. Due to the fact that the mechanism of RyR1 remodelling under exercise conditions were proven to be similar in mice and humans, a comparable effect of JTV-519 and S-107 on trained athletes is expected, making the compounds relevant for doping controls. After synthesis of JTV-519, S-107, and a putative desmethylated metabolite of S-107, target compounds were characterized using nuclear magnetic resonance spectroscopy and electrospray ionization (ESI),high-resolution/high-accuracy Orbitrap mass spectrometry. Collision-induced dissociation pathways were suggested based on the determination of elemental compositions of product ions and H/D-exchange experiments. The most diagnostic product ion of JTV-519 was found at m/z 188 (representing the 4-benzyl-1-methyl piperidine residue), and S-107 as well as its desmethylated analog yielded characteristic fragments at m/z 153 and 138 (accounting for 1-methoxy-4-methylsulfanyl-benzene and 4-methoxy-benzenethiol residues, respectively). The analytes were implemented in existing doping control screening procedures based on liquid chromatography, multiple reaction monitoring and simultaneous precursor ion scanning modes using a triple quadrupole mass spectrometer. Validation items such as specificity, recovery (68,92%), lower limit of detection (0.1,0.2 ng/mL), intraday (5.2,18.5%) and interday (8.7,18.8%) precision as well as ion suppression/enhancement effects were determined. Copyright © 2009 John Wiley & Sons, Ltd. [source]

Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010
Ling Wang
Abstract Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

linear free energy relationships;

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 11 2007
UB3LYP/6-31G(d
The substituent effect on the reactivity of the CN bond of molecular ions of 4-substituted N -(2-furylmethyl)anilines toward two dissociation pathways was studied. With this aim, six of these compounds were analyzed by mass spectrometry using electron ionization with energies between 7.8 and 69.9 eV. Also, the UB3LYP/6-31G (d,p) and UHF/6-31G (d, p) levels of theory were used to calculate the critical energies (reaction enthalpies at 0 K) of the processes that lead to the complementary ions [C5H5O]+ and [M , C5H5O]+, assuming structures that result from the heterolytic and homolytic CN bond cleavages of the molecular ions, respectively. A kinetic approach proposed in the 1960s was applied to the mass spectral data to obtain the relative rate coefficients for both dissociation channels from ratios of the peak intensities of these ions. Linear relationships were obtained between the logarithms of the relative rate coefficients and the calculated critical energies and other thermochemical properties, whose slopes showed to be conditioned by the energy provided to the compounds within the ion source. Moreover, it was found that the dissociation that leads to [C5H5O]+ is a process strongly dependent upon the electron withdrawing or donating properties of the substituent, favored by those factors that destabilize the molecular ion. On the contrary, the dissociation that leads to [M , C5H5O]+ is indifferent to the polar electronic effects of the substituent. The abundance of both products was governed by the rule of Stevenson,Audier, according to which the major ion is the one of less negative electronic affinity. Copyright © 2007 John Wiley & Sons, Ltd. [source]