| 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. |
- Caldararu, Octav, et al.
(författare)
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QM/MM study of the reaction mechanism of sulfite oxidase
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39-49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.
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| 3. |
- 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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| 4. |
- Li, Jilai, et al.
(författare)
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Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction
- 2013
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:3, s. 1799-1807
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Tidskriftsartikel (refereegranskat)abstract
- The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated Basis sets of at least triple-zeta quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD (T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBEO, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.
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| 5. |
- 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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| 6. |
- Ryde, Ulf, et al.
(författare)
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Computational Studies of Molybdenum and Tungsten Enzymes
- 2016. - 7
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Ingår i: Molybdenum and Tungsten Enzymes: Spectroscopic and Theoretical Investigations. - Cambridge : Royal Society of Chemistry. - 2045-547X. - 9781782628781 - 9781782628842 ; 2017-January:7, s. 275-321
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Bokkapitel (refereegranskat)abstract
- We review computational studies of three important mono-nuclear molybdenum oxo-transfer enzymes, dimethylsulfoxide reductase, sulfite oxidase and xanthine oxidase. We show that calculated energies for these reactions are very sensitive to details in the calculations, in particular to the density-functional method employed and the size of the basis set, but the treatment of dispersion and solvation effects is also crucial, as well as the definition of the reference state. We point out problems with standard quantum-mechanical (QM) cluster calculations, regarding the selection of the QM system and atomic coordinate constraints. Combined QM and molecular mechanics (QM/MM) methods also have important problems, which can be solved by calculations with very large QM systems (400-1000 atoms). Many studies have been published that reproduce experimentally measured activation energies, but for the wrong reason. We also compare the properties of molybdenum and tungsten and discuss why the active sites of the three families of molybdenum oxo-transfer enzymes are so different.
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| 7. |
- Ryde, Ulf, et al.
(författare)
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Does DFT-D estimate accurate energies for the binding of ligands to metal complexes?
- 2011
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9234 .- 1477-9226. ; 40:Online 19 Aug 2011, s. 11176-11183
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the homolytic dissociation of a methyl radical from a model of methyl cobalamin. For this reaction, density functional theory with an atom-pairwise dispersion correction (DFT-D) gives a dispersion contribution to the bond dissociation energy (BDE) of 22-51 kJ mol(-1) depending on the functional, i.e. much more than common estimates for the total dispersion interaction energy of the methyl group in typical solvents. We show that this large energy correction results from many rather small (0-2 kJ mol(-1)) interactions that arise between the ligand and the metal and the other ligands when a short metal-ligand bond is formed. The energy terms result mostly from atom pairs connected by two or three bonds, i.e. terms that normally are ignored or scaled down at the molecular mechanics level, and have large contributions from r(-8) terms. The added dispersion energy diminishes the variation in the calculated BDE observed among various generalised-gradient approximation (GGA) functionals, whereas a gap still persists between the results of GGA and hybrid functionals. Model calculations at the local MP2 and CCSD (second-order perturbation theory and coupled cluster theory with single and double excitations) levels are in a similar range as the dispersion interactions estimated by DFT-D (23-29 kJ mol(-1)). However, both the DFT-D and the wavefunction-based results include middle-range correlation effects that vary greatly between different DFT methods owing to their different density-based description in the short-range regime. Therefore, it is not meaningful to discuss which DFT method gives the most accurate estimate of the dispersion contribution to the BDE. Moreover, for a balanced treatment of dispersion during the binding reaction in solution, the dispersion energy of the ligand and the unbound complex with the surroundings needs also to be considered, which decreases the net dispersion contribution to binding by ~20 kJ mol(-1).
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| 8. |
- 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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