| 1. |
- Delcey, Mickaël G., 1988-, et al.
(författare)
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Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase
- 2014
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 16:17, s. 7927-7938
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the geometry and singlet-triplet energy difference of two mono-nuclear Ni2+ models related to the active site in [NiFe] hydrogenase. Multiconfigurational second-order perturbation theory based on a complete active-space wavefunction with an active space of 12 electrons in 12 orbitals, CASPT2(12,12), reproduces experimental bond lengths to within 1 pm. Calculated singlet-triplet energy differences agree with those obtained from coupled-cluster calculations with single, double and (perturbatively treated) triple excitations (CCSD(T)) to within 12 kJ mol(-1). For a bimetallic model of the active site of [NiFe] hydrogenase, the CASPT2(12,12) results were compared with the results obtained with an extended active space of 22 electrons in 22 orbitals. This is so large that we need to use restricted active-space theory (RASPT2). The calculations predict that the singlet state is 48-57 kJ mol(-1) more stable than the triplet state for this model of the Ni-Sl(a) state. However, in the [NiFe] hydrogenase protein, the structure around the Ni ion is far from the square-planar structure preferred by the singlet state. This destabilises the singlet state so that it is only similar to 24 kJ mol(-1) more stable than the triplet state. Finally, we have studied how various density functional theory methods compare to the experimental, CCSD(T), CASPT2, and RASPT2 results. Semi-local functionals predict the best singlet-triplet energy differences, with BP86, TPSS, and PBE giving mean unsigned errors of 12-13 kJ mol(-1) (maximum errors of 25-31 kJ mol(-1)) compared to CCSD(T). For bond lengths, several methods give good results, e. g. TPSS, BP86, and M06, with mean unsigned errors of 2 pm for the bond lengths if relativistic effects are considered.
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| 2. |
- Karlström, Gunnar, et al.
(författare)
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MOLCAS : a program package for computational chemistry
- 2003
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Ingår i: Computational materials science. - 0927-0256 .- 1879-0801. ; 28:2, s. 222-239
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Tidskriftsartikel (refereegranskat)abstract
- The program system MOLCAS is a package for calculations of electronic and structural properties of molecular systems in gas, liquid, or solid phase. It contains a number of modern quantum chemical methods for studies of the electronic structure in ground and excited electronic states. A macromolecular environment can be modeled by a combination of quantum chemistry and molecular mechanics. It is further possible to describe a crystalline material using model potentials. Solvent effects can be treated using continuum models or by combining quantum chemical calculations with molecular dynamics or Monte-Carlo simulations. MOLCAS is especially adapted to treat systems with a complex electronic structure, where the simplest quantum chemical models do not work. These features together with the inclusion of relativistic effects makes it possible to treat with good accuracy systems including atoms from the entire periodic system. MOLCAS has effective methods for geometry optimization of equilibria, transition states, conical intersections, etc. This facilitates studies of excited state energy surfaces, spectroscopy, and photochemical processes.
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| 3. |
- Lindh, Roland, et al.
(författare)
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On the significance of the trigger reaction in the action of the calicheamicin γI 1 anti-cancer drug
- 1997
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 97:1, s. 203-210
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Tidskriftsartikel (refereegranskat)abstract
- The significance of the so-called trigger reaction in the reaction mechanism of the calicheamicin γI 1 anti-cancer drug has been studied with ab initio quantum chemical methods. The structures of four fragments of calicheamicin γI 1, consisting of either 39 or 41 atoms, have been fully optimized using the Becke-Perdew86 density functional method and the 6-31G* basis sets. The four structures constitute members of an isodesmic reaction for which the reaction energy is a direct measure of the change in activation energy of the Bergman reaction, caused by the structural rearrangements of the preceding trigger reaction. This difference in activation energy has been calculated with density functional theory, using the exchange-correlation functional mentioned above, and with second-order Møller-Plesset perturbation theory (MP2), employing an ANO-type basis set. In both cases a value of 12 kcal/ mol is obtained. The study firmly supports the hypothesis that the significance of the trigger reaction is to saturate a double bond in the vicinity of the enediyne group, which counteracts the formation of the biradical state of the drug. The MP2 computations became feasible by a novel implementation of an integral-direct, distributed-data, parallel MP2 algorithm.
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| 4. |
- Söderhjelm, Pär, et al.
(författare)
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Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models
- 2007
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 28:6, s. 1083-1090
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Tidskriftsartikel (refereegranskat)abstract
- Localized multipole moments up to the fifth moment as well as localized dipole polarizabilities are calculated with the MpProp and the newly developed LoProp methods for a total of 20 molecules, predominantly derived from amino acids. A comparison of electrostatic potentials calculated from the multipole expansion obtained by the two methods with ab initio results shows that both methods reproduce the electrostatic interaction with an elementary charge with a mean absolute error of similar to 1.5 kJ/mol at contact distance and less than 0.1 kJ/mol at distances 2 angstrom further out when terms up to the octupole moments are included. The polarizabilities are tested with homogenous electric fields and are-found to have similar accuracy. The MpProp method gives better multipole moments unless diffuse basis sets are used, whereas LoProp gives better polarizabilities. (C) 2007 Wiley Periodicals, Inc.
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