An ONIOM investigation of the effect of conformation on bond dissociation energies in peptides

Chan, Bun; Radom, Leo

doi:10.1002/jcc.25538

Cited by 6 publications

(4 citation statements)

References 60 publications

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“…We previously found MS1-D3 to be reasonable for geometry optimizations; in addition, the energetic consequences of using geometries optimized with different functionals are not excessive. − We also determined that the DSD-PBEP86 DH-DFT method is highly accurate for obtaining conformational energies of similar systems. , In passing, we note that the related revDSD-PBEP86 method yields results that are generally comparable to or somewhat better than those for DSD-PBEP86, which we also found in some other cases . Nonetheless, herein we use the DSD-PBEP86//MS1-D3 relative energies on the basis of our initial assessment of closely related systems.…”

Section: Resultssupporting

confidence: 66%

Modeling the Conformational Preference of the Lignocellulose Interface and Its Interaction with Weak Acids

2022

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We have examined the conformational space of model systems for the hydrogen-bonded and covalent linkages between the sugar and lignin components of lignocellulose. Specifically, glucose and paracoumaryl alcohol moieties are used in our models. Multistage screening protocols are used to identify and validate a set of lowest-energy isomers. We found a cost-effective screening process involving an initial screening with DFTB3/3ob using a 20 kJ mol–1 threshold, a refinement with the SCANh/6-31+G(2d,p) method with a 10 kJ mol–1 cutoff, a third step at the DSD-PBEP86/ma-def2-TZVP//MS1-D3/6-31+G(2d,p) level with the same 10 kJ mol–1 threshold, and a last step at the CCSD(T)/CBS//B3LYP/cc-pVTZ level with a tighter 5 kJ mol–1 threshold. The use of machine learning (with the London and Axilrod–Teller–Muto potential) can further accelerate the screening process. In general, all low-energy conformers are characterized by hydrogen bonding between the sugar and lignin moieties. We examined the interactions of covalently bonded sugar–lignin models with weak acids (HSO3 –, H2PO3 –, HSeO3 –, H2citrate–, etc.) and found that they interacted strongly with the oxygen of the sugar–O–lignin linkage. Our results suggest that acids such as dihydrogen citrate may be attractive alternatives to the commonly used HSO3 – for lignocellulose processing.

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Section: Resultssupporting

confidence: 66%

Modeling the Conformational Preference of the Lignocellulose Interface and Its Interaction with Weak Acids

2022

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“…We have used a random subset of conformers to examine the use of several methods for geometry optimization. Our benchmark geometries were obtained in the gas phase at the B3-LYP-D3BJ/maug-cc-pVTZ level. − In our previous studies, we find that the energetic consequences of using geometries optimized with different functionals are not excessive. , The lower level methods that we have examined include B3-LYP-D3BJ with a variety of smaller basis sets, the N12 nonhybrid DFT method with the 6-31G(d) basis set, the AM1 and PM7 semiempirical methods, and the MM2 and MMFF molecular mechanics methods. Our assessment involves comparing single-point energies obtained with benchmark geometries with those obtained using lower level structures.…”

Section: Computational Detailsmentioning

confidence: 99%

Aqueous-Phase Conformations of Lactose, Maltose, and Sucrose and the Assessment of Low-Cost DFT Methods with the DSCONF Set of Conformers for the Three Disaccharides

Chan

2020

J. Phys. Chem. A

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In the present study, we have examined a range of quantum chemistry methods for the calculation of conformers for lactose, maltose, and sucrose. We find that the DSD-PBE-P86/ aug′-cc-pVTZ//B3-LYP-D3BJ/6-311+G(2d,p) protocol yields good relative energies in comparison with reference CCSD(T)/CBS//B3-LYP-D3BJ/maug-cc-pVTZ values. We have surveyed a total of ∼550 conformers for the three disaccharides with the chosen DSD-PBE-P86 method in conjunction with continuum aqueous solvation. In each case, the lowest free energy conformer is characterized by hydrogen bond(s) between the two rings. Another finding is that the major contributors to the overall variations in aqueous free energies are the electronic energies and the solvation energies. To facilitate investigations of larger systems, we have compiled the DSCONF set of conformers for the three disaccharides, and we have assessed lower cost methods with this set. We find MS1-D3/6-31+G(2d,p) to be cost-effective and accurate for both geometry optimization and the calculation of relative energies for disaccharides. In addition, we note that MS1-D3 has previously been found to yield good relative energies for the WATER27 set of water clusters. We thus deem this method to be appropriate for the study of saccharide conformations in both gas phase and aqueous solution.

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“…Because no significant deviation from the X-ray structure was observed in the dynamics simulation with the exception of thermal fluctuation, the PRS snapshots closest to the transition state obtained by the theozyme models were extracted from the AMBER formula for the grid inhomogeneous solvation theory (GIST) as the starting geometries in the ONIOM calculations. At first, the whole structure from the NPT ensemble was partially truncated so that only the catalytic center with the 6 Å neighborhood of core residues, E136, Y46, and H102, were preoptimized at the empirical-molecular mechanics level (PM7) with the constraint of partially formed C–O bonds for fast screening spiro- and fused-transition states . The calculated fused- S and spiro- R systems included 84 atoms for the high layer and respectively 4113 and 4109 atoms for the low layer, and among them 1591 and 1574 atoms within the fully optimized 6 Å active pocket range.…”

Section: Computational Detailsmentioning

confidence: 99%

“…At first, the whole structure from the NPT ensemble was partially truncated so that only the catalytic center with the 6 Å neighborhood of core residues, E136, Y46, and H102, were preoptimized at the empirical-molecular mechanics level (PM7) with the constraint of partially formed C−O bonds for fast screening spiro-and fused-transition states. 43 The calculated fused-S and spiro-R systems included 84 atoms for the high layer and respectively 4113 and 4109 atoms for the low layer, and among them 1591 and 1574 atoms within the fully optimized 6 Å active pocket range. The transition structures then were fully optimized with high-level QM methods with the ωB97X-D functional 26 and standard Pople style 6-31+G(d) basis sets for the QM region.…”

Section: Introductionmentioning

confidence: 99%

Computational Exploration of How Enzyme XimE Converts Natural S-Epoxide to Pyran and R-Epoxide to Furan

Jiang

Zhao

et al. 2021

ACS Catal.

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Enzymes have long been characterized for their specificity and efficiency in catalyzing one substrate to one product. However, a SnoaL-like cyclase (XimE) that was originally discovered in xiamenmycin biosynthesis not only catalyzes the pyran-forming cyclization of the natural epoxide metabolites generated by XimD, but also enhances the furan-forming cyclization of the unnatural epoxide isomer. We have investigated and elucidated the reaction mechanism for this potentially unique substrate control of enzyme function. We explored the plausible pathways occurring at the hydrophobic active sites with a combination of theozyme (a small cluster model) calculations, pre- and post-reaction molecular dynamics (MD) simulations, ONIOM(ωB97X-D/6-31G(d):AMBER) transition state searching, and QM/SCRF(VS) dielectric constant scanning. Both the pyran and furan pathways share similar general acid–base catalytic mechanisms in which E136 and H102 act as proton donor and acceptor, respectively; pyran is generated by a fused-TS that proceeds via a general-acid-catalyzed mode, while furan is generated via a spiro-TS catalyzed by a general-base-catalyzed mode. The relative energies of the four possible transition states were found by ONIOM calculations to be Fused-S ≲ Spiro-S < Spiro-R < Fused-R. The regiochemical preference of the XimE-catalyzed pyran formation from S-epoxide and furan formation from R-epoxide stems from the induced-fit interaction between the enzyme and its transition states, which carries over to products. XimE apparently evolved along with the natural S-epoxide substrate generated by the upstream XimD epoxidase, and accidentally is also able to catalyze a different reaction of the enantiomeric R-epoxide via a similar catalytic mechanism.

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An ONIOM investigation of the effect of conformation on bond dissociation energies in peptides

Cited by 6 publications

References 60 publications

Modeling the Conformational Preference of the Lignocellulose Interface and Its Interaction with Weak Acids

Modeling the Conformational Preference of the Lignocellulose Interface and Its Interaction with Weak Acids

Aqueous-Phase Conformations of Lactose, Maltose, and Sucrose and the Assessment of Low-Cost DFT Methods with the DSCONF Set of Conformers for the Three Disaccharides

Computational Exploration of How Enzyme XimE Converts Natural S-Epoxide to Pyran and R-Epoxide to Furan

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