Acylation and deacylation mechanism of Helicobacter pylori AmiF formamidase: A computational DFT study

He, Rongxing; Yang, Qinlei; Li, Ming

doi:10.1016/j.cplett.2014.02.005

Cited by 4 publications

(1 citation statement)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fixed-atom constraints invariably give rise to a large number of imaginary vibrational frequencies upon structure relaxation. − These have been noted in numerous publications, − yet a satisfactory explanation has never been provided. Their magnitude is typically small, being variously reported (for the modes exhibiting negative curvature) as |ν| ∼ 10 cm –1 , − |ν| ≲ 20 cm –1 , − |ν| ≲ 30 cm –1 , ,− |ν| ≲ 40 cm –1 , − |ν| ≤ 50 cm –1 , …”

Section: Introductionmentioning

confidence: 99%

Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites

Bowling,

Dasgupta,

Herbert

2024

J. Chem. Inf. Model.

View full text Add to dashboard Cite

In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Fulldimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.

show abstract