Ab initio MO study on model compounds of malonyl-CoA: malonic acid and malonyl methyl sulfide

Han, Sang-Jae; Kim, Young Ju; Kang, Young Kee

doi:10.1016/s0166-1280(96)04595-2

Cited by 6 publications

(7 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The 6-31G* optimized geometries of the −CSCOCH 3 moiety of acetyl-MEA are in good agreement with those of methyl thioformate determined from infrared and microwave experiments and those of methyl thioacetate and ethyl thiopropanoate optimized at the HF/6-31++G* level . The optimized geometries of the malonyl sulfide moiety at the 6-31G* level are also in accord with those of the malonyl sulfide anion optimized recently by us at the HF/6-31G** and HF/6-31+G** levels …”

Section: Resultssupporting

confidence: 82%

“…This implies that this hydrogen bond appears to lead the most preferred conformation of malonyl-MEA to be different from that of MEA or acetyl-MEA. In addition, the loss of preferred conformations for the torsion angle φ 5 of the malonyl methyl sulfide anion, studied by us previously, supports the important role of this hydrogen bond in determining the preferred conformations of malonyl-MEA.…”

Section: Resultssupporting

confidence: 73%

“…See the text for details. For hydrogen malonate, acetic acid, and H 2 O, these quantities were calculated for the lowest energy conformations, whose starting conformations were taken from the results of ref obtained at the HF/6-31G** level. b HF energies in hartrees; 1 hartree = 627.509 551 6 kcal/mol.…”

Section: Resultsmentioning

confidence: 99%

“…The necessary quantities to calculate the free energy changes of hydrolysis are listed in Table , which correspond to statistically weighted values for low-energy conformations of MEA, acetyl-MEA, and malonyl-MEA at the 6-31G* level, as described later. The values of hydrogen malonate, acetic acid, and H 2 O were calculated for their lowest energy conformations optimized at the same basis set, which were started from lowest energy conformations optimized at the HF/6-31G** level − in order to figure out solvation effects on the hydrolysis.…”

Section: Resultsmentioning

confidence: 99%

“…To a torsion angle φ 4 of acetyl-MEA, three values of ±60° and 180° were initially assigned. The three minimum-energy conformations of the malonyl sulfide anion optimized at the HF/6-31G** level were used as initial values of torsion angles φ 4 , φ 5 , and φ 6 of malonyl-MEA. Thus, the 30 conformations were chosen as starting points for the HF/3-21G geometry optimization of acetyl-MEA and malonyl-MEA.…”

Section: Methodsmentioning

confidence: 99%

See 4 more Smart Citations

Ab Initio Molecular Orbital Calculations on N-β-Mercaptoethylacetamide and Its Derivatives as Model Compounds of Coenzyme A (CoA), Acetyl-CoA, and Malonyl-CoA

Kang

Han

1997

J. Phys. Chem. B

Self Cite

View full text Add to dashboard Cite

The conformational study on N-β-mercaptoethylacetamide (MEA), acetyl-MEA, and malonyl-MEA as model compounds of coenzyme A (CoA), acetyl-CoA, and malonyl-CoA, respectively, is carried out using the ab initio method at the HF/6-31G* level and the hydration shell model in order to investigate the information on structures and energetics of the compounds when acetyl-CoA or malonyl-CoA is hydrolyzed into acetic acid and CoA or hydrogen malonate and CoA, respectively, in the gas phase and in solution. It is found that the overall preferred conformations of MEA are different from those of acetyl-MEA or malonyl-MEA and that the intramolecular hydrogen bond between amide hydrogen and terminal carboxylate oxygen is responsible for the low-energy conformations of malonyl-MEA. To determine the thermodynamic parameters in the gas phase at 298.15 K, the vibrational analysis was undertaken for minimized conformations. The preferred conformations and structural parameters of the three compounds are in accord with those of related compounds obtained from spectroscopic experiments and are reasonably consistent with the corresponding data of CoA and its derivatives complexed with CoA-binding proteins deduced from X-ray and NMR studies to within experimental uncertainty. For the hydrolysis of acetyl-MEA and malonyl-MEA in aqueous solution, total free energy changes (ΔG tot) are computed to be −12.4 and −22.5 kcal/mol, respectively, of which the former is in good agreement with the experimental value of −13.8 ± 0.1 kcal/mol for the hydrolysis of acetyl-CoA. Although computed free energy changes (ca. −15 kcal/mol) for the two reactions in the gas phase are almost the same, the hydration appears to raise and lower the ΔG tot for the hydrolysis of acetyl-MEA and malonyl-MEA, respectively. The more negative value of ΔG tot for the hydrolysis of malonyl-MEA in solution implies that the malonyl-CoA may have a higher group transfer potential than the acetyl-CoA.

show abstract

Section: Resultssupporting

confidence: 82%

Section: Resultssupporting

confidence: 73%

Section: Resultsmentioning

confidence: 99%