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Donald G Truhlar - One of the best experts on this subject based on the ideXlab platform.
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a new local density functional for main group thermochemistry Transition metal bonding thermochemical kinetics and noncovalent interactions
2006Co-Authors: Yan Zhao, Donald G TruhlarAbstract:We present a new local density functional, called M06-L, for main-group and Transition Element thermochemistry, thermochemical kinetics, and noncovalent interactions. The functional is designed to capture the main dependence of the exchange-correlation energy on local spin density, spin density gradient, and spin kinetic energy density, and it is parametrized to satisfy the uniform-electron-gas limit and to have good performance for both main-group chemistry and Transition metal chemistry. The M06-L functional and 14 other functionals have been comparatively assessed against 22 energetic databases. Among the tested functionals, which include the popular B3LYP, BLYP, and BP86 functionals as well as our previous M05 functional, the M06-L functional gives the best overall performance for a combination of main-group thermochemistry, thermochemical kinetics, and organometallic, inorganometallic, biological, and noncovalent interactions. It also does very well for predicting geometries and vibrational frequencies. Because of the computational advantages of local functionals, the present functional should be very useful for many applications in chemistry, especially for simulations on moderate-sized and large systems and when long time scales must be addressed. © 2006 American Institute of Physics. DOI: 10.1063/1.2370993
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databases for Transition Element bonding metal metal bond energies and bond lengths and their use to test hybrid hybrid meta and meta density functionals and generalized gradient approximations
2005Co-Authors: Nathan E Schultz, Yan Zhao, Donald G TruhlarAbstract:We propose a data set of bond lengths for 8 selected Transition metal dimers (Ag2, Cr2, Cu2, CuAg, Mo2, Ni2, V2, and Zr2) and another data set containing their atomization energies and the atomization energy of ZrV, and we use these for testing density functional theory. The molecules chosen for the test sets were selected on the basis of the expected reliability of the data and their ability to constitute a diverse and representative set of Transition Element bond types while the data sets are kept small enough to allow for efficient testing of a large number of computational methods against a very reliable subset of experimental data. In this paper we test 42 different functionals: 2 local spin density approximation (LSDA) functionals, 12 generalized gradient approximation (GGA) methods, 13 hybrid GGAs, 7 meta GGA methods, and 8 hybrid meta GGAs. We find that GGA density functionals are more accurate for the atomization energies of pure Transition metal systems than are their meta, hybrid, or hybrid me...
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databases for Transition Element bonding metal metal bond energies and bond lengths and their use to test hybrid hybrid meta and meta density functionals and generalized gradient approximations
2005Co-Authors: Nathan E Schultz, Yan Zhao, Donald G TruhlarAbstract:We propose a data set of bond lengths for 8 selected Transition metal dimers (Ag(2), Cr(2), Cu(2), CuAg, Mo(2), Ni(2), V(2), and Zr(2)) and another data set containing their atomization energies and the atomization energy of ZrV, and we use these for testing density functional theory. The molecules chosen for the test sets were selected on the basis of the expected reliability of the data and their ability to constitute a diverse and representative set of Transition Element bond types while the data sets are kept small enough to allow for efficient testing of a large number of computational methods against a very reliable subset of experimental data. In this paper we test 42 different functionals: 2 local spin density approximation (LSDA) functionals, 12 generalized gradient approximation (GGA) methods, 13 hybrid GGAs, 7 meta GGA methods, and 8 hybrid meta GGAs. We find that GGA density functionals are more accurate for the atomization energies of pure Transition metal systems than are their meta, hybrid, or hybrid meta analogues. We find that the errors for atomization energies and bond lengths are not as large if we limit ourselves to dimers with small amounts of multireference character. We also demonstrate the effects of increasing the fraction of Hartree-Fock exchange in multireference systems by computing the potential energy curve for Cr(2) and Mo(2) with several functionals. We also find that BLYP is the most accurate functional for bond energies and is reasonably accurate for bond lengths. The methods that work well for Transition metal bonds are found to be quite different from those that work well for organic and other main group chemistry.
Yan Zhao - One of the best experts on this subject based on the ideXlab platform.
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a new local density functional for main group thermochemistry Transition metal bonding thermochemical kinetics and noncovalent interactions
2006Co-Authors: Yan Zhao, Donald G TruhlarAbstract:We present a new local density functional, called M06-L, for main-group and Transition Element thermochemistry, thermochemical kinetics, and noncovalent interactions. The functional is designed to capture the main dependence of the exchange-correlation energy on local spin density, spin density gradient, and spin kinetic energy density, and it is parametrized to satisfy the uniform-electron-gas limit and to have good performance for both main-group chemistry and Transition metal chemistry. The M06-L functional and 14 other functionals have been comparatively assessed against 22 energetic databases. Among the tested functionals, which include the popular B3LYP, BLYP, and BP86 functionals as well as our previous M05 functional, the M06-L functional gives the best overall performance for a combination of main-group thermochemistry, thermochemical kinetics, and organometallic, inorganometallic, biological, and noncovalent interactions. It also does very well for predicting geometries and vibrational frequencies. Because of the computational advantages of local functionals, the present functional should be very useful for many applications in chemistry, especially for simulations on moderate-sized and large systems and when long time scales must be addressed. © 2006 American Institute of Physics. DOI: 10.1063/1.2370993
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databases for Transition Element bonding metal metal bond energies and bond lengths and their use to test hybrid hybrid meta and meta density functionals and generalized gradient approximations
2005Co-Authors: Nathan E Schultz, Yan Zhao, Donald G TruhlarAbstract:We propose a data set of bond lengths for 8 selected Transition metal dimers (Ag2, Cr2, Cu2, CuAg, Mo2, Ni2, V2, and Zr2) and another data set containing their atomization energies and the atomization energy of ZrV, and we use these for testing density functional theory. The molecules chosen for the test sets were selected on the basis of the expected reliability of the data and their ability to constitute a diverse and representative set of Transition Element bond types while the data sets are kept small enough to allow for efficient testing of a large number of computational methods against a very reliable subset of experimental data. In this paper we test 42 different functionals: 2 local spin density approximation (LSDA) functionals, 12 generalized gradient approximation (GGA) methods, 13 hybrid GGAs, 7 meta GGA methods, and 8 hybrid meta GGAs. We find that GGA density functionals are more accurate for the atomization energies of pure Transition metal systems than are their meta, hybrid, or hybrid me...
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databases for Transition Element bonding metal metal bond energies and bond lengths and their use to test hybrid hybrid meta and meta density functionals and generalized gradient approximations
2005Co-Authors: Nathan E Schultz, Yan Zhao, Donald G TruhlarAbstract:We propose a data set of bond lengths for 8 selected Transition metal dimers (Ag(2), Cr(2), Cu(2), CuAg, Mo(2), Ni(2), V(2), and Zr(2)) and another data set containing their atomization energies and the atomization energy of ZrV, and we use these for testing density functional theory. The molecules chosen for the test sets were selected on the basis of the expected reliability of the data and their ability to constitute a diverse and representative set of Transition Element bond types while the data sets are kept small enough to allow for efficient testing of a large number of computational methods against a very reliable subset of experimental data. In this paper we test 42 different functionals: 2 local spin density approximation (LSDA) functionals, 12 generalized gradient approximation (GGA) methods, 13 hybrid GGAs, 7 meta GGA methods, and 8 hybrid meta GGAs. We find that GGA density functionals are more accurate for the atomization energies of pure Transition metal systems than are their meta, hybrid, or hybrid meta analogues. We find that the errors for atomization energies and bond lengths are not as large if we limit ourselves to dimers with small amounts of multireference character. We also demonstrate the effects of increasing the fraction of Hartree-Fock exchange in multireference systems by computing the potential energy curve for Cr(2) and Mo(2) with several functionals. We also find that BLYP is the most accurate functional for bond energies and is reasonably accurate for bond lengths. The methods that work well for Transition metal bonds are found to be quite different from those that work well for organic and other main group chemistry.
Ralf R. Mendel - One of the best experts on this subject based on the ideXlab platform.
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The Molybdenum Cofactor
2013Co-Authors: Ralf R. MendelAbstract:The Transition Element molybdenum needs to be complexed by a special cofactor to gain catalytic activity. Molybdenum is bound to a unique pterin, thus forming the molybdenum cofactor (Moco), which, in different variants, is the active compound at the catalytic site of all molybdenum-containing enzymes in nature, except bacterial molybdenum nitrogenase. The biosynthesis of Moco involves the complex interaction of six proteins and is a process of four steps, which also require iron, ATP, and copper. After its synthesis, Moco is distributed, involving Moco-binding proteins. A deficiency in the biosynthesis of Moco has lethal consequences for the respective organisms.
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molybdenum cofactor biosynthesis in plants and humans
2011Co-Authors: Ralf R. Mendel, Gunter SchwarzAbstract:Abstract The Transition Element molybdenum (Mo) needs to be complexed by a special cofactor in order to gain catalytic activity. With the exception of bacterial Mo-nitrogenase, where Mo is a constituent of the FeMo-cofactor, Mo is bound to a pterin, thus forming the molybdenum cofactor Moco, which in different variants is the active compound at the catalytic site of all other Mo-containing enzymes. The biosynthesis of Moco involves the complex interaction of six proteins and is a process of four steps, which also requires reducing equivalents, iron, ATP and probably copper. After its synthesis, Moco is distributed to the apoproteins of Mo-enzymes by Moco–carrier/binding proteins that also participate in Moco-insertion into the cognate apoproteins. A deficiency in the biosynthesis of Moco has lethal consequences for the respective organisms. In humans, Moco deficiency is a severe inherited inborn error in metabolism resulting in severe neurodegeneration in newborns and causing early childhood death. Due to our better understanding of the chemistry of Moco synthesis, a first therapy has been brought to the clinic.
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Biology of the molybdenum cofactor
2007Co-Authors: Ralf R. MendelAbstract:The Transition Element molybdenum (Mo) is an essential micronutrient for plants where it is needed as a catalytically active metal during enzyme catalysis. Four plant enzymes depend on molybdenum: nitrate reductase, sulphite oxidase, xanthine dehydrogenase, and aldehyde oxidase. However, in order to gain biological activity and fulfil its function in enzymes, molybdenum has to be complexed by a pterin compound thus forming the molybdenum cofactor. In this article, the path of molybdenum from its uptake into the cell, via formation of the molybdenum cofactor and its storage, to the final modification of the molybdenum cofactor and its insertion into apo-metalloenzymes will be reviewed.
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molybdoenzymes and molybdenum cofactor in plants
1999Co-Authors: Ralf R. Mendel, Gunter SchwarzAbstract:The Transition Element molybdenum is essential for (nearly) all organisms and occurs in more than 30 enzymes catalyzing diverse redox reactions; however, only three Mo-enzymes have been found in plants so far. (1) Nitrate reductase catalyzes the key step in inorganic nitrogen assimilation, (2) aldehyde oxidase(s) recently have been shown to catalyze the last step in the biosynthesis of the phytohormones indole acetic acid and abscisic acid, respectively, and (3) xanthine dehydrogenase is involved in purine catabolism. These enzymes are homodimeric proteins harboring an electron transport chain that involves different prosthetic groups (FAD, heme, or Fe-S, Mo). Among different Mo-enzymes, the alignment of amino acid sequences helps to define regions that are well conserved (domains) and other regions that are highly variable in sequence (interdomain hinge regions). The existence of additional plant Mo-enzymes (like sulfite oxidase) also has to be considered. In this review we focus on structure-function re...
Nathan E Schultz - One of the best experts on this subject based on the ideXlab platform.
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databases for Transition Element bonding metal metal bond energies and bond lengths and their use to test hybrid hybrid meta and meta density functionals and generalized gradient approximations
2005Co-Authors: Nathan E Schultz, Yan Zhao, Donald G TruhlarAbstract:We propose a data set of bond lengths for 8 selected Transition metal dimers (Ag2, Cr2, Cu2, CuAg, Mo2, Ni2, V2, and Zr2) and another data set containing their atomization energies and the atomization energy of ZrV, and we use these for testing density functional theory. The molecules chosen for the test sets were selected on the basis of the expected reliability of the data and their ability to constitute a diverse and representative set of Transition Element bond types while the data sets are kept small enough to allow for efficient testing of a large number of computational methods against a very reliable subset of experimental data. In this paper we test 42 different functionals: 2 local spin density approximation (LSDA) functionals, 12 generalized gradient approximation (GGA) methods, 13 hybrid GGAs, 7 meta GGA methods, and 8 hybrid meta GGAs. We find that GGA density functionals are more accurate for the atomization energies of pure Transition metal systems than are their meta, hybrid, or hybrid me...
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databases for Transition Element bonding metal metal bond energies and bond lengths and their use to test hybrid hybrid meta and meta density functionals and generalized gradient approximations
2005Co-Authors: Nathan E Schultz, Yan Zhao, Donald G TruhlarAbstract:We propose a data set of bond lengths for 8 selected Transition metal dimers (Ag(2), Cr(2), Cu(2), CuAg, Mo(2), Ni(2), V(2), and Zr(2)) and another data set containing their atomization energies and the atomization energy of ZrV, and we use these for testing density functional theory. The molecules chosen for the test sets were selected on the basis of the expected reliability of the data and their ability to constitute a diverse and representative set of Transition Element bond types while the data sets are kept small enough to allow for efficient testing of a large number of computational methods against a very reliable subset of experimental data. In this paper we test 42 different functionals: 2 local spin density approximation (LSDA) functionals, 12 generalized gradient approximation (GGA) methods, 13 hybrid GGAs, 7 meta GGA methods, and 8 hybrid meta GGAs. We find that GGA density functionals are more accurate for the atomization energies of pure Transition metal systems than are their meta, hybrid, or hybrid meta analogues. We find that the errors for atomization energies and bond lengths are not as large if we limit ourselves to dimers with small amounts of multireference character. We also demonstrate the effects of increasing the fraction of Hartree-Fock exchange in multireference systems by computing the potential energy curve for Cr(2) and Mo(2) with several functionals. We also find that BLYP is the most accurate functional for bond energies and is reasonably accurate for bond lengths. The methods that work well for Transition metal bonds are found to be quite different from those that work well for organic and other main group chemistry.
Weng Kee Leong - One of the best experts on this subject based on the ideXlab platform.
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binuclear oxidative addition of sb cl bonds a facile synthetic route to main group Transition Element clusters and rings
2014Co-Authors: Rakesh Ganguly, Weng Kee LeongAbstract:Binuclear oxidative addition of Sb–Cl bonds with the clusters Os3(CO)11(NCCH3), 1, or Os3(CO)10(NCCH3)2, 2, was found to be an effective synthetic route to organometallic clusters and rings containing μ2-SbPh2 or μ3-SbPh moieties. Thus, the reaction of SbPh2Cl with 1 afforded the tetranuclear ring Os3(CO)11(Cl)(μ-SbPh2), 3, while its reaction with 2 afforded the pentanuclear ring Os3(CO)10(Cl)2(μ-SbPh2)2, 6. In each case, two or three isomeric products were isolated depending on the reaction conditions. The analogous reaction of SbPhCl2 with 1, on the other hand, afforded the spiked triangular cluster Os3(CO)11(Cl)2(μ3-SbPh), 7, which also existed as two isomers. Pathways for these reactions have been proposed, and the experimental and computational evidence presented.
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metal metal bond opening toward main group Transition Element rings
2001Co-Authors: Weng Kee Leong, Guizhu ChenAbstract:The reaction of the cluster Os6(μ4-Sb)(μ-H)2(μ-SbPh2)(μ3,η2-C6H4)(μ3,η4-C12H8)(CO)15, 1, with excess tBuNC resulted in ring expansion via metal−metal bond cleavage to afford the novel compounds Os6(μ4-Sb)(μ-H)(μ-SbPh2)(C6H5)(μ3,η4-C12H8)(CO)14(CNtBu)4, 2, and Os6(μ4-Sb)(μ-H)(μ-SbPh2)(C6H5)(μ3,η4-C12H8)(CO)15(CNtBu)3, 3, both of which contain five-membered Os3Sb2 rings.
