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Volumn 133, Issue 9, 2011, Pages 2904-2915

Dinuclear Zn(II) complex catalyzed phosphodiester cleavage proceeds via a concerted mechanism: A density functional theory study

Author keywords

[No Author keywords available]

Indexed keywords

A-DENSITY; BASE CATALYSIS; BINDING MODES; BOND FORMATION; CLEAVAGE REACTION; CONCERTED MECHANISM; DENSITY FUNCTIONAL THEORY CALCULATIONS; DIANIONS; DINUCLEAR; EXPERIMENTAL OBSERVATION; EXPERIMENTAL VALUES; GROUP COORDINATES; HIGHER-ENERGY BARRIERS; KINETIC ISOTOPE EFFECTS; LEAVING GROUPS; NITROPHENYL PHOSPHATES; NUCLEOPHILIC ATTACK; PHOSPHODIESTERS; PHOSPHORYL OXYGEN; PRESENCE/ABSENCE; RATE DETERMINING STEP; REACTION BARRIERS; STEP TRANSITIONS; WATER MOLECULE; ZINC IONS; ZN COMPLEX;

EID: 79952270966     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja106456u     Document Type: Article
Times cited : (59)

References (116)
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    • NBO analysis was performed using the NBO Version 3.1, as implemented in the Gaussian 03 package by Glendening, E. D.; Badenhoop, J. K.; Reed, A. E.; Carpenter, J. E.; Weinhold, F.
    • NBO analysis was performed using the NBO Version 3.1, as implemented in the Gaussian 03 package by Glendening, E. D.; Badenhoop, J. K.; Reed, A. E.; Carpenter, J. E.; Weinhold, F.
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    • note
    • m are the rate constant, Boltzmann constant, Planck constant, universal gas constant, absolute temperature and active free energy in the standard state of a mole particles, respectively.
  • 107
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    • In the absence of catalyst, the EIEs (1.0245 and 1.0002) for deprotonation of HpPNP were calculated using the program ISOEFF98 with PCM/B3LYP/6-31+G(d,p) by Hengge and co-workers (ref 28). We also recalculated the EIEs at the level of PCM/B3LYP/6-31G(d,p) within the harmonic oscillator/rigid rotor approximations, as implemented in the Gaussian 03 program. Our results are similar to the values of ref 28.
    • In the absence of catalyst, the EIEs (1.0245 and 1.0002) for deprotonation of HpPNP were calculated using the program ISOEFF98 with PCM/B3LYP/6-31+G(d,p) by Hengge and co-workers (ref 28). We also recalculated the EIEs at the level of PCM/B3LYP/6-31G(d,p) within the harmonic oscillator/rigid rotor approximations, as implemented in the Gaussian 03 program. Our results are similar to the values of ref 28.
  • 110
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    • +
    • +.
  • 113
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    • a values (ref 67) are about 13, and in 298.15K, the rough free energy change values are approximately estimated to be about 17.7 kcal/mol.
    • a values (ref 67) are about 13, and in 298.15K, the rough free energy change values are approximately estimated to be about 17.7 kcal/mol.
  • 114
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    • The sum of the bond orders to the nucleophile and leaving group is less than 1 in a loose transition state, while this sum is greater than 1 in a tight (or associative) transition state (see refs 54a and 54c for details).
    • The sum of the bond orders to the nucleophile and leaving group is less than 1 in a loose transition state, while this sum is greater than 1 in a tight (or associative) transition state (see refs 54a and 54c for details).
  • 115
    • 79952256191 scopus 로고    scopus 로고
    • The orbital interaction energies are roughly estimated by the second order perturbation theory analysis of the Fock Matrix in a NBO basis.
    • The orbital interaction energies are roughly estimated by the second order perturbation theory analysis of the Fock Matrix in a NBO basis.
  • 116
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    • In Fan and Gao's work (ref 45), the TPSS density functional theory (with density fitting functions included) was employed. The basis set 6-31++G(d′,p′) was used for N, O, aromatic C, and all H atoms bound to N and O, while 6-31G was used for alkyl C and the rest of all H atoms, SDD was used for Zn atoms, and LANL2DZ plus a d-polarization, and a p-diffuse function was used for P atom.
    • In Fan and Gao's work (ref 45), the TPSS density functional theory (with density fitting functions included) was employed. The basis set 6-31++G(d′,p′) was used for N, O, aromatic C, and all H atoms bound to N and O, while 6-31G was used for alkyl C and the rest of all H atoms, SDD was used for Zn atoms, and LANL2DZ plus a d-polarization, and a p-diffuse function was used for P atom.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.