Understanding cross‐boundary events in ONIOM QM:QM' calculations

Lundberg, Marcus

doi:10.1002/jcc.21982

Cited by 3 publications

(3 citation statements)

References 33 publications

(40 reference statements)

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“…SCC‐DFTB has been adopted in the study of enzymatic systems to describe the lower level of the ONIOM method scheme (instead of using MM for the lower level as in typical QM/MM schemes), or in QM/MM calculations, where it describes the QM level of the studied systems, mostly in QM/MM molecular dynamics, coupled with umbrella sampling calculations . In the present system, the performance of SCC‐DFTB in the geometry of our system is similar to the GGA or LDA functionals, with a MUE of 0.09 Å (Supporting Information Table S2).…”

Section: Resultsmentioning

confidence: 99%

“…Despite these results, recent works point out that inclusion of D3 dispersion leads to the improvement of molecular geometries, a result that is more significant in larger systems and smaller basis sets. [110,111] SCC-DFTB has been adopted in the study of enzymatic systems to describe the lower level of the ONIOM method scheme (instead of using MM for the lower level as in typical QM/MM schemes), [112,113] or in QM/MM calculations, where it describes the QM level of the studied systems, mostly in QM/MM molecular dynamics, coupled with umbrella sampling calculations. [113][114][115][116][117] In the present system, the performance of SCC-DFTB in the geometry of our system is similar to the GGA or LDA functionals, with a MUE of 0.09 Å (Supporting Information Table S2).…”

Section: Geometry Benchmarkingmentioning

confidence: 99%

See 1 more Smart Citation

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

Pereira

Ribeiro

Fernandes

et al. 2017

Int J of Quantum Chemistry

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In recent years, there has been an increased interest in understanding the enzymatic mechanism of glycosidases resorting mostly to DFT and DFT/MM calculations. However, the performance of density functionals (DFs) is well known to be system and property dependent. Trends drawn from general studies, despite important to evaluate the quality of the DFs and to pave the way for the development of new DFs, may be misleading when applied to a single specific system/property. To overcome this issue, we carried out a benchmarking study of 40 DFs applied to the geometry optimization and to the electronic barrier height (EBarrier) and electronic energy of reaction (ER) of prototypical glycosidase‐catalyzed reactions. Additionally, we report calculations with SCC‐DFTB and four semiempirical MO methods applied to the same problem. We have used a universal molecular model for retaining glycosidases, comprising only a 22‐atoms system that mimics the active site and substrate. High accuracy reference geometries and energies were calculated at the CCSD(T)/CBS//MP2/aug‐cc‐pVTZ level of theory. Most DFs reproduce the reference geometries extremely well, with mean unsigned errors (MUE) smaller than 0.05 Å for bond lengths and 3° for bond angles. Among the DFs, wB97X‐D, CAM‐B3LYP, B3P86, and PBE1PBE have the best performance in geometry optimizations (MUE = 0.02 Å). Conversely, semiempirical MO and SCC‐DFTB methods yielded less accurate geometries (MUE between 0.09 and 0.17 Å). The inclusion of D3 correction has a small, but still relevant, influence in the geometry predicted by some DFs. Regarding EBarrier, 11 DFs (MPW1B95, CAM‐B3LYP, M06 ‐ 2X, PBE1PBE, wB97X ‐ D, B1B95, BMK, MN12 – SX, M05, M06, and M11) presented errors below 1 kcal.mol−1, in relation to the reference energy. Most of these functionals belong to the family of hybrid functionals (H‐GGA, HH‐GGA, and HM‐GGA), which shows a positive influence of HF exchange in the determination of EBarrier. The inclusion of D3 correction has not affected significantly the EBarrier and ER. The use of geometries at the accurate but expensive MP2/aug‐cc‐pVTZ level of theory has a small, albeit not insignificant, influence in the EBarrier when compared with energies calculated with geometries determined with the DFs (usually a few tenths of kcal.mol−1, with exceptions). In general, semiempirical MO methods and DFTB are associated with larger errors in the determination of EBarrier, with unsigned errors from 6.9 to 24.7 kcal.mol−1.

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Section: Resultsmentioning

confidence: 99%

Section: Geometry Benchmarkingmentioning

confidence: 99%

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

Pereira

Ribeiro

Fernandes

et al. 2017

Int J of Quantum Chemistry

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show abstract

“…This is expected to give a better interaction of the model part and the low-level system as both are treated at quantum mechanical level. 46 The CASSCF-based higher level of theory has been treated with 4 active electrons in 4 active orbitals, considering the C-N-O moiety as the core region (model) of our photochemical interest which involves the C-N p bond and the p z orbital on oxygen in the nitrone-oxaziridine photo-conversion process. The total energy in the ONIOM methodology is expressed through an extrapolation scheme:…”

Section: Computational Detailsmentioning

confidence: 99%

A comprehensive spectroscopic investigation of α-(2-naphthyl)-N-methylnitrone: a computational study on photochemical nitrone–oxaziridine conversion and thermal E–Z isomerization processes

Saini

Chattopadhyay

2015

RSC Adv.

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This comprehensive spectroscopic analysis of a-(2-naphthyl)-N-methylnitrone has proposed its photochemical oxaziridine formation and thermal E-Z isomerization mechanisms. The activation energy for the conversion of the unstable non-planar E isomer to the stable planar Z-isomer is found to be 23.7 kcal mol À1 at the CASSCF/6-31G* level of calculation. A transition state with a negative frequency of 350 cm À1 is likely to be responsible for this process. Both CASSCF and ONIOM-based studies have revealed that the nitrone-oxaziridine photochemical conversion involves non-radiative decay channels which include biradicaloid conical intersection (CI) points through Hula-twist and terminal one-bond-flip motions, situated at 35-40 kcal mol À1 below the first excited singlet state (S 1 ). Following the directions of their gradient-difference vectors, the optimized oxaziridine geometries are obtained. The nature of the low-lying singlet-singlet transitions of these a-naphthyl N-methylnitrones is found to be similar to that of the conjugated non-polar polyenes, and differs appreciably from our previously studied longchain conjugated nitrone systems. The fluorescent S 1 state with a radiative lifetime of nanosecond order is populated by the weak upward S 0 -S 1 transition (transition moment: 0.3 Debye) and through the decay of the S 2 state, which eventually gets involved in the S 0 /S 1 conical intersections.

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Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases

KellieJennifer

Wetmore

2013

Can. J. Chem.

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When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.

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Understanding cross‐boundary events in ONIOM QM:QM' calculations

Cited by 3 publications

References 33 publications

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

A comprehensive spectroscopic investigation of α-(2-naphthyl)-N-methylnitrone: a computational study on photochemical nitrone–oxaziridine conversion and thermal E–Z isomerization processes

Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases

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