| 1. |
- Andrejic, Milica, et al.
(författare)
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Coupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems
- 2014
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Ingår i: ChemPhysChem. - : Wiley. - 1439-7641 .- 1439-4235. ; 15:15, s. 3270-3281
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a method to calculate interaction energies of large systems (such as host-guest or even protein-ligand systems) at the local coupled-cluster with singles, doubles, and perturbative triples level, and with extrapolation to the limit of a complete basis set. The method is based on the polarizable multipole interactions with supermolecular pairs molecular fractionation approach, which combines a pairwise quantum-mechanical evaluation of the short-range interactions with a polarizable multipole treatment of many-body effects. The method is tested for nine guest molecules binding to an octa-acid host (in total 198-207 atoms), as part of the SAMPL4 blind challenge. From the test calculations, the accuracy of the approach is found to be 10 kJ mol(-1) or better. Comparison with dispersion-corrected density functional theory reveals that the latter underestimates the dispersion contribution for this type of system, which leads to a difference in the ranking of the ligands.
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| 2. |
- Li, Jilai, et al.
(författare)
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A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulfoxide Reductase with Mo and W
- 2015
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Ingår i: European Journal of Inorganic Chemistry. - : Wiley. - 1099-0682 .- 1434-1948. ; :21, s. 3580-3589
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Tidskriftsartikel (refereegranskat)abstract
- A thorough computational study has been performed to investigate oxygen atom transfer (OAT) reactions catalyzed by dimethyl sulfoxide reductase (DMSOR) with a catalytic molybdenum or tungsten ion. Thirteen different density functional theory (DFT) methods have been employed to obtain structural parameters along the reaction pathway, and single-point energies were computed with local correlation coupled-cluster methods [LCCSD(T0)]. For both Mo and W, most DFT methods indicate that the enzyme follows a twostep mechanism with a stable intermediate in which a DMSO molecule coordinates to the metal ion in the +IV oxidation state, and this is also confirmed by the LCCSD(T0) energies. The W-substituted models have a 26-30 kJ/mol lower activation barrier for the OAT reaction, and the reaction is 6370 kJ/mol more exothermic than that with Mo. Different DFT methods give widely different activation and reaction energies, which roughly depend on the amount of exact exchange in the method; these differences are also reflected in the structures, especially for the rate-limiting transition state. Consequently, there is quite a large variation in energies and various energy corrections (thermal, solvation, dispersion, and relativistic; up to 39 kJ/mol) depending on which DFT method is used to obtain the geometries. Therefore, a mechanism predicted by a single method should be viewed with caution.
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| 3. |
- Mikulskis, Paulius, et al.
(författare)
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Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies.
- 2014
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Ingår i: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 1573-4951 .- 0920-654X. ; 28:4, s. 375-400
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Tidskriftsartikel (refereegranskat)abstract
- We have estimated free energies for the binding of nine cyclic carboxylate guest molecules to the octa-acid host in the SAMPL4 blind-test challenge with four different approaches. First, we used standard free-energy perturbation calculations of relative binding affinities, performed at the molecular-mechanics (MM) level with TIP3P waters, the GAFF force field, and two different sets of charges for the host and the guest, obtained either with the restrained electrostatic potential or AM1-BCC methods. Both charge sets give good and nearly identical results, with a mean absolute deviation (MAD) of 4 kJ/mol and a correlation coefficient (R (2)) of 0.8 compared to experimental results. Second, we tried to improve these predictions with 28,800 density-functional theory (DFT) calculations for selected snapshots and the non-Boltzmann Bennett acceptance-ratio method, but this led to much worse results, probably because of a too large difference between the MM and DFT potential-energy functions. Third, we tried to calculate absolute affinities using minimised DFT structures. This gave intermediate-quality results with MADs of 5-9 kJ/mol and R (2) = 0.6-0.8, depending on how the structures were obtained. Finally, we tried to improve these results using local coupled-cluster calculations with single and double excitations, and non-iterative perturbative treatment of triple excitations (LCCSD(T0)), employing the polarisable multipole interactions with supermolecular pairs approach. Unfortunately, this only degraded the predictions, probably because of a mismatch between the solvation energies obtained at the DFT and LCCSD(T0) levels.
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| 4. |
- Van Severen, Marie-Céline, et al.
(författare)
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A quantum-mechanical study of the reaction mechanism of sulfite oxidase.
- 2014
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 1432-1327 .- 0949-8257. ; 19:7, s. 1165-1179
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Tidskriftsartikel (refereegranskat)abstract
- The oxidation of sulfite to sulfate by two different models of the active site of sulfite oxidase has been studied. Both protonated and deprotonated substrates were tested. Geometries were optimized with density functional theory (TPSS/def2-SV(P)) and energies were calculated either with hybrid functionals and large basis sets (B3LYP/def2-TZVPD) including corrections for dispersion, solvation, and entropy, or with coupled-cluster theory (LCCSD(T0)) extrapolated toward a complete basis set. Three suggested reaction mechanisms have been compared and the results show that the lowest barriers are obtained for a mechanism where the substrate attacks a Mo-bound oxo ligand, directly forming a Mo-bound sulfate complex, which then dissociates into the products. Such a mechanism is more favorable than mechanisms involving a Mo-sulfite complex with the substrate coordinating either by the S or O atom. The activation energy is dominated by the Coulomb repulsion between the Mo complex and the substrate, which both have a negative charge of -1 or -2.
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