Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase

Erdtman, Edvin; Bushnell, Eric A. C.; Gauld, James W.; Eriksson, Leif A.

doi:10.1016/j.comptc.2010.11.015

Cited by 25 publications

(34 citation statements)

References 30 publications

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“…Moreover, the neutralization of the anionic Glu-COO À in I2 would be unflavored. Hence, this instability of I2 at the ONIOM(MP2/6-31G(d)//HF/6-31G(d):AMBER94)-EE level of theory suggests that it may instead represent a transition structure for Glu-COO À -assisted proton transfer from -Glu NH 2 + -to the carbinolamine hydroxyl oxygen, which would otherwise have required an unfavorable fourmembered ring transition structure (Almasi et al, 2011;Erdtman et al, 2011;Hall & Smith, 1998a). Moreover, the involvement of the carboxylate group is comparable to previous studies (Hall & Smith, 1998b;Rosenberg, Silver, Sayer, & Jencks, 1974;Williams, 1987) in which water assists the proton transfer from the bridging -NH 2 + -to the carbinolamine oxygen resulting in lower barriers.…”

Section: Saccharopine Reductasementioning

confidence: 97%

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations

Bushnell

Berryman

Gauld

et al. 2015

Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions

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Section: Saccharopine Reductasementioning

confidence: 97%

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations

Bushnell

Berryman

Gauld

et al. 2015

Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions

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“…[40,41,44,46] The energy barrier of 34.6-32.4 kcal mol -1 for the hemiaminal formation step resembles the values calculated for the reaction between ammonia and formaldehyde (34.2 kcal mol -1 B3LYP/6-311++G(d,p), [44] 33.5 kcal mol -1 G3B3 composite method [46] ) or between acetone and methylamine (32.7 kcal mol -1 ), [41] formaldehyde and phenylamine (31.8 kcal mol -1 B3LYP/6-311++G(2d,2p)), [45] but is higher than for the reaction between formaldehyde and methylamine or vinylamine (24.8 kcal mol -1 and 24.4 kcal mol -1 , respectively). [40,41,44,46] The energy barrier of 34.6-32.4 kcal mol -1 for the hemiaminal formation step resembles the values calculated for the reaction between ammonia and formaldehyde (34.2 kcal mol -1 B3LYP/6-311++G(d,p), [44] 33.5 kcal mol -1 G3B3 composite method [46] ) or between acetone and methylamine (32.7 kcal mol -1 ), [41] formaldehyde and phenylamine (31.8 kcal mol -1 B3LYP/6-311++G(2d,2p)), [45] but is higher than for the reaction between formaldehyde and methylamine or vinylamine (24.8 kcal mol -1 and 24.4 kcal mol -1 , respectively).…”

Section: Computational Detailsmentioning

confidence: 99%

Internal Hydrogen Bond Influences the Formation of [2+2] Schiff Base Macrocycle: Open‐Chain Vs. Hemiaminal and Macrocycle Forms

2019

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Open‐chain vs. hemiaminal and macrocycle forms of the condensation product of 2,6‐diformylpyridine and opposite enantiomers of trans‐1,2‐diaminocyclopentane have been studied using DFT methods to reveal that the macrocycle (with a water molecule co‐product) is the thermochemically preferred form. The mechanistic picture of formation of [[2+2]] Schiff base macrocycle from its chain precursor has been supplemented with the electron localization function analysis revealing the crucial electronic aspects underlying the covalent bonds evolution. The macrocycle formation may proceed along two paths, through two distinct diastereoisomerc hemiaminal intermediates. The reaction rate limiting water elimination step exhibits the considerably lower and unusually flat energy barrier for the path involving S hemiaminal due to the strong decoupling of the CO bond cleavage from the proton migration to form the water molecule.

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“…Schiff bases are well‐known compounds and are commonly used in industrial and biological area as a reaction intermediate. The possible reaction mechanism of the Schiff base formation and the effect of the solvent effect, pH, and type of reactants have also been explained theoretically .…”

Section: Introductionmentioning

confidence: 99%

Density Functional Study of the Reaction Mechanism of Two Oxiimine Alcohol Formations and Their Novel Rearrangements

Kaya

2016

Helvetica Chimica Acta

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In this study, the reaction mechanisms of isonitrosoacetophenone (inapH) with ethanolamine (ea) and 1‐phenylethanolamine (pea) have been investigated theoretically using B3LYP/6‐311G(d,p) method to explain why the formation and unexpected rearrangement products occur or not occur. While the reaction between isonitrosoacetophenone (inapH) with ethanolamine gives oximine alcohol (Ib), the reaction of 1‐phenylethanolamine with inapH results in the formation of oximine alcohol with a different substituent (Ia) and amido alcohol (IIa), which is the unexpected rearrangement product. The rearrangement driving forces of compounds from Ia to IIa are calculated as ca. 28 and 23 kJ/mol in the gas and EtOH phases, respectively. These driving forces have been calculated ca. 46 and 45 kJ/mol for the rearrangement of compound Ib to obtain IIb in the same phases, respectively. This high driving force shows that the compound IIb cannot be obtained from rearrangement of compound Ib as described experimentally in the literature. In addition, as the DFT functionals poorly describe dispersion effects, dispersion correction for reaction heat and free‐energy barrier was estimated using the wB97X‐D/6‐311G(d,p). In general, the relative free energies of all molecules calculated from wB97XD method are lower than performed from B3LYP level. The changes of thermodynamic properties for all molecules with temperature ranging from 100 to 500 K have been obtained using the statistical thermodynamic method.

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Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase

Cited by 25 publications

References 30 publications

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations

Internal Hydrogen Bond Influences the Formation of [2+2] Schiff Base Macrocycle: Open‐Chain Vs. Hemiaminal and Macrocycle Forms

Density Functional Study of the Reaction Mechanism of Two Oxiimine Alcohol Formations and Their Novel Rearrangements

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