A comparative study of DFT and traditional ab initio methodologies on the OsO4 molecule

Ujaque, Gregori; Maseras, Feliu; Lleds, Agust

doi:10.1002/(sici)1097-461x(2000)77:2<544::aid-qua6>3.0.co;2-l

Cited by 9 publications

(5 citation statements)

References 58 publications

(25 reference statements)

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“…The ionization potential of OsO 4 is calculated to be 13.02 eV, which is very close to the experimental value 12.97 ± 0.12 eV from the mass spectrometric study . Previous theoretical work also showed that for the OsO 4 molecule the B3LYP results could give satisfactory descriptions on the geometry and vibrational frequencies, being in good agreement with CCSD(T) results and experimental data. Later in this paper we will take the dehydration of methane by OsO + as an example to further calibrate the selected method by comparison with the UCCSD(T) method.…”

Section: Computational Detailssupporting

confidence: 83%

Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsO_n⁺ (n = 1−4) with Methane

Zhang

Jiang

2004

Organometallics

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The sextet, quartet, and doublet potential energy surfaces (PESs) of the reactions of methane with gas-phase OsO n + (n=1−4) have been explored via density functional calculations to investigate the mechanisms of these reactions. For the reactions of OsO n + (n = 1−2) with methane, the minimum energy reaction paths are found to involve two spin inversions in the entrance and exit channels. Specifically, they are most likely to proceed through the following steps: 4OsO+ + CH4 → 2OOsCH4 + → 2OOs(H)CH3 + → 2OOsH(H)(CH2)+ → 4OOs(CH2)+ + H2; and 4OsO2 + + CH4 → 2O(O)OsCH4 + → 2O(O)Os(H)CH3 + → 2O(HO)Os(CH3)+ → 2O(HO)Os(H)(CH2)+ → 2OOs(H2O)(CH2)+ → 4OOs(CH2)+ + H2O, respectively. Along the minimum energy pathway the exothermicity of the overall reaction would be 17.3 kcal/mol for OsO+ + CH4 → OOs(CH2)+ + H2, and 24.0 kcal/mol for OsO2 + + CH4 → OOs(CH2)+ + H2O. For the reaction of OsO3 + with methane, it is found to be kinetically unfavorable at room temperature because the intermediate generated by the activation of the first C−H bond has a significantly positive Gibbs free energy relative to the reactants. For OsO4 +, our calculations suggest that it can readily react with methane on the doublet PES by a direct hydrogen atom abstraction process, and the whole reaction is exothermic by 31.8 kcal/mol. These results agree with the experimental observation that OsO n + (n = 1−2, 4) can readily activate methane but OsO3 + cannot.

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Section: Computational Detailssupporting

confidence: 83%

Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsO_n⁺ (n = 1−4) with Methane

Zhang

Jiang

2004

Organometallics

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“…The theories tested include Hartree-Fock (HF), second-order Møller-Plesset (MP2), Slater exchange functional with the Vosko-Wilk-Nusiar correlation functional (S-VWN), B3-LYP, B3-P86, and B-VWN. Since addition of polarization functions on both metal and atoms involved in π-bonding to the metal has been shown to significantly affect the geometry of the metal, 37 they were included in the basis sets tested, which ranged from 6-31+G(d) to 6-311++G(2d,2p) (see below and Table 1). The theory/basis set that reproduced the X-ray structure of bis-(ethane-1,2dithiolato-S,S′)-zinc(II) was then employed to predict the structure of [Zn(HS) 4 ] 2and [Zn(CH 3 S) 4 ] 2-.…”

Section: Methodsmentioning

confidence: 99%

Modeling Zn²⁺−Cysteinate Complexes in Proteins

Dudev

Lim

2001

J. Phys. Chem. B

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Before computational results can be reliably interpreted, it is critical to calibrate the theoretical calculations with respect to appropriate experimental data. Such calibrations have been carried out for biologically important zinc-cysteinate complexes in this work. Calculations using different quantum mechanical methods were carried out to determine the theory/basis set that can reproduce the X-ray structure of a zinc-cysteinate-like complex and the measured gas-phase deprotonation free energy of H 2 S. The S-VWN/6-311++G(d,p) method was found to reproduce the X-ray geometry of bis-(ethane-1,2-dithiolato-S,S′)-zinc(II). In particular, it yielded an average Zn-S bond distance of 2.34 Å for bis-(ethane-1,2-dithiolato-S,S′)-zinc(II) and [Zn(CH 3 S -) 4 ] 2-, in excellent agreement with experiment. In contrast, B3-LYP with the same basis set overestimated the average Zn-S bond distance by about 0.1 Å. With the 6-311++G(d,p) basis set, MP2 and post-MP2 methods could reproduce the experimental gas-phase deprotonation free energy of H 2 S, while DFT methods such as B3-LYP and S-VWN yielded less accurate values. Furthermore, a set of effective radii for zinc and atoms of water and HSconsistent with S-VWN/6-311++G(d,p) geometries and NBO charges as well as MP2/6-311++G(d,p)//S-VWN/6-311++G(d,p) energies has been obtained. These radii predicted the correct free energy of Zn 2+ binding to dianionic 2,3-dimercapto-1-propanol in solution. The results obtained here should help in modeling the structural and thermodynamical properties of zinc-cysteinate binding sites. Moreover, the strategy described in this work could be applied in modeling other metal-binding sites in proteins.

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“…Compared with the rich studies on the FeO x system, the Ru and Os analogs have received much less attention, except for the well-known tetroxides. − The RuO molecule has been studied spectroscopically in the gas phase and in solid matrices. ,− The ground state was determined to be a 5 Δ state. − ,, No spectroscopic data is available for the osmium monoxide. DFT calculations predict that a 5 Σ + state and a 3 Φ state are very close in energy. , Both the ruthenium and osmium dioxide and trioxide molecules have been observed in solid matrices. , The RuO 2 molecule was predicted to have a 1 A 1 ground state with a bond angle close to 150°. , From the isotopic frequencies for the ν 3 mode in solid neon, the upper and low limits of the RuO 2 bond angle were estimated to be 169° and 151° .…”

Section: Neutral Mononuclear Transition Metal Oxides and Dioxygen Com...mentioning

confidence: 99%

Spectroscopic and Theoretical Studies of Transition Metal Oxides and Dioxygen Complexes

2009

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A comparative study of DFT and traditional ab initio methodologies on the OsO4 molecule

Cited by 9 publications

References 58 publications

Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsO_n⁺ (n = 1−4) with Methane

Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsO_n⁺ (n = 1−4) with Methane

Modeling Zn²⁺−Cysteinate Complexes in Proteins

Spectroscopic and Theoretical Studies of Transition Metal Oxides and Dioxygen Complexes

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A comparative study of DFT and traditional ab initio methodologies on the OsO4 molecule

Cited by 9 publications

References 58 publications

Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsOn+ (n = 1−4) with Methane

Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsOn+ (n = 1−4) with Methane

Modeling Zn2+−Cysteinate Complexes in Proteins

Spectroscopic and Theoretical Studies of Transition Metal Oxides and Dioxygen Complexes

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Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsO_n⁺ (n = 1−4) with Methane

Density Functional Study on the Mechanisms of the Reactions of Gas-Phase OsO_n⁺ (n = 1−4) with Methane

Modeling Zn²⁺−Cysteinate Complexes in Proteins