The Experts below are selected from a list of 4704 Experts worldwide ranked by ideXlab platform
Michele Parrinello - One of the best experts on this subject based on the ideXlab platform.
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ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
1995Co-Authors: Mark E Tuckerman, Kari Laasonen, Michiel Sprik, Michele ParrinelloAbstract:Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interAtomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen Atoms, including the excess proton, are treated as classical particles with the mass of a Deuterium Atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlik...
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ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
1995Co-Authors: Mark E Tuckerman, Kari Laasonen, Michiel Sprik, Michele ParrinelloAbstract:Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interAtomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen Atoms, including the excess proton, are treated as classical particles with the mass of a Deuterium Atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlike (H7O4)− complex. Transport of the charge defects is a concerted dynamical process coupling proton transfer along hydrogen bonds and reorganization of the local environment. The simulation results strongly support the structural diffusion mechanism for charge transport. In this model, the entire structure—and not the constituent particles—of the charged complex migrates through the hydrogen bond network. For H3O+, we propose that transport of the excess proton is driven by coordination fluctuations in the first solvation shell (i.e., second solvation shell dynamics). The rate‐limiting step for OH− diffusion is the formation of the (H7O4)− structure, which is the solvation state showing proton transfer activity.
David Ohagan - One of the best experts on this subject based on the ideXlab platform.
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incorporation of 2h1 1r 2r and 2h1 1s 2r glycerols into the antibiotic nucleocidin in streptomyces calvus
2017Co-Authors: Xuan Feng, Nawaf Al Maharik, Axel Bartholome, Jeffrey E Janso, Usa Reilly, David OhaganAbstract:Deuterium incorporations from [2H1]-(1R,2R) and [2H1]-(1S,2R) glycerols into the fluorine containing antibiotic nucleocidin, in Streptomyces calvus indicate that one Deuterium Atom is incorporated at the C-5′ site of nucleocidin from each of these isotopomers of glycerol. Two Deuteriums become incorporated at C-5′ of nucleocidin after a feeding experiment with [2H5]-glycerol. These observations indicate that there is no obligate oxidation of the pro-R hydroxymethyl group of glycerol as it progresses through the pentose phosphate pathway and becomes incorporated into the fluorinated antibiotic.
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biosynthesis of fluoroacetate and 4 fluorothreonine in streptomyces cattleya incorporation of oxygen 18 from 2 2h 2 18o glycerol and the role of serine metabolites in fluoroacetaldehyde biosynthesis
2001Co-Authors: David Ohagan, Christoph Schaffrath, Cormac D Murphy, John T G HamiltonAbstract:A series of isotope labelling experiments was carried out to investigate the biosynthesis of fluoroacetate and 4-fluorothreonine in resting cells of Streptomyces cattleya. Previous studies have shown that fluoroacetaldehyde is a precursor to both of these metabolites and the experiments were conducted to explore in greater detail the metabolic origin of fluoroacetaldehyde in S. cattleya. Ethanolamine and cysteamine are C2 metabolites of serine and cysteine respectively and these two metabolites emerged as candidate precursors to fluoroacetaldehyde in S. cattleya. However feeding experiments with [1,1-2H2]-ethanolamine and [1,1-2H2]-cysteamine did not indicate incorporation into the fluorometabolites, suggesting that these compounds are not relevant precursors to fluoroacetaldehyde in S. cattleya. Upon feeding [2-2H,2-18O]-glycerol to resting cells of S. cattleya, the Deuterium Atom was not incorporated into 4-fluorothreonine, however the oxygen-18 Atom became incorporated into the carboxylate group of fluoroacetate and into the C(3)-O oxygen Atom of 4-fluorothreonine. This observation indicates that there is an oxidation at C-2 of glycerol, but that the oxygen Atom is formally retained from glycerol during the biosynthesis. In overview, the data suggest that fluoroacetaldehyde is derived from a C3 glycolytic intermediate rather than a C2 amino acid metabolite.
Kari Laasonen - One of the best experts on this subject based on the ideXlab platform.
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ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
1995Co-Authors: Mark E Tuckerman, Kari Laasonen, Michiel Sprik, Michele ParrinelloAbstract:Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interAtomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen Atoms, including the excess proton, are treated as classical particles with the mass of a Deuterium Atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlik...
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ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
1995Co-Authors: Mark E Tuckerman, Kari Laasonen, Michiel Sprik, Michele ParrinelloAbstract:Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interAtomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen Atoms, including the excess proton, are treated as classical particles with the mass of a Deuterium Atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlike (H7O4)− complex. Transport of the charge defects is a concerted dynamical process coupling proton transfer along hydrogen bonds and reorganization of the local environment. The simulation results strongly support the structural diffusion mechanism for charge transport. In this model, the entire structure—and not the constituent particles—of the charged complex migrates through the hydrogen bond network. For H3O+, we propose that transport of the excess proton is driven by coordination fluctuations in the first solvation shell (i.e., second solvation shell dynamics). The rate‐limiting step for OH− diffusion is the formation of the (H7O4)− structure, which is the solvation state showing proton transfer activity.
Kenji Fueki - One of the best experts on this subject based on the ideXlab platform.
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rate constant for the tunneling reaction hydrogen Deuterium Atom fwdarw hydrogen Atom hydrogen deuteride in the solid Deuterium hydrogen mixture at 4 k
1992Co-Authors: Tetsuo Miyazaki, Susumu Kitamura, Hiroyuki Morikita, Kenji FuekiAbstract:Amounts of D and H Atoms, produced by γ-radiolysis of D 2 -n-H 2 (1 mol %) mixtures, were measured at 4.2 or 1.9 K by ESR. The amounts of D Atoms decay upon storage of the irradiated sample at 4.2 K up to 114 hn while those of H Atoms are nearly constant. The results were interpreted in terms of competition of a tunneling reaction n-H 2 +D→H+HD with combination reactions of D and H Atoms. Similar decay behaviors of D and H Atoms were also observed in D 2 -p-H 2 (l mol %) mixtures at 4.2 K and D 2 -n-H 2 (1 mol %) mixtures at 4.5 K
Mark E Tuckerman - One of the best experts on this subject based on the ideXlab platform.
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ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
1995Co-Authors: Mark E Tuckerman, Kari Laasonen, Michiel Sprik, Michele ParrinelloAbstract:Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interAtomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen Atoms, including the excess proton, are treated as classical particles with the mass of a Deuterium Atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlik...
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ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
1995Co-Authors: Mark E Tuckerman, Kari Laasonen, Michiel Sprik, Michele ParrinelloAbstract:Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interAtomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen Atoms, including the excess proton, are treated as classical particles with the mass of a Deuterium Atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlike (H7O4)− complex. Transport of the charge defects is a concerted dynamical process coupling proton transfer along hydrogen bonds and reorganization of the local environment. The simulation results strongly support the structural diffusion mechanism for charge transport. In this model, the entire structure—and not the constituent particles—of the charged complex migrates through the hydrogen bond network. For H3O+, we propose that transport of the excess proton is driven by coordination fluctuations in the first solvation shell (i.e., second solvation shell dynamics). The rate‐limiting step for OH− diffusion is the formation of the (H7O4)− structure, which is the solvation state showing proton transfer activity.