Multiscale Modelling of Lytic Polysaccharide Monooxygenases

Lytic polysaccharide monooxygenase (LPMO) enzymes have attracted considerable attention due to their ability to enhance polysaccharide depolymerization, making them interesting in respect to production of biofuel from cellulose. The LPMOs are metalloenzymes that contain a mononuclear copper active site that can active dioxygen. However, many details of this activation are unclear, and have previously been investigated from a computational angle. Yet, these studies have either employed only molecular mechanics (MM), which are inaccurate for metal active sites, or they have described only the active site with quantum mechanics (QM) and neglected the effect of the protein. Here, we employ hybrid QM and MM (QM/MM) methods to investigate the first steps of the LPMO mechanism, which is reduction of of Cu(II) to Cu(I) and formation of a Cu(II)-superoxide complex. In the latter complex, the superoxide can bind either in an equatorial or an axial position. For both steps we obtain structures that are markedly different from previous suggestions, based on vacuum calculations. Our calculations show that the equatorial isomer of the superoxide complex is over 60 kJ/mol more stable than the axial isomer, being stabilized by interactions with a second-coordination-sphere Gln residue, showing a possible role for this residue. Coordination of superoxide in this manner is in agreement with recent experimental suggestions.Comment: 21 pages, 6 figures, 3 tables. 20 pages Supporting Informatio

Molecular mechanism of lytic polysaccharide monooxygenases

The lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism and hence boost generation of biofuel from e.g. cellulose. By employing density functional theory in a combination of quantum mechanics and molecular mechanics (QM/MM), we report a complete description of the molecular mechanism of LPMOs. The QM/MM scheme allows us to describe all reaction steps with a detailed protein environment and we show that this is necessary. Several active species capable of abstracting a hydrogen from the substrate have been proposed previously. We investigate previously suggested paths as well as new ones. We describe the generation of the reactive intermediates, the abstraction of a hydrogen atom from the polysaccharide substrate, as well as the final recombination step in which OH is transferred back to the substrate. We show that a superoxo [CuO2]+ complex can be protonated by a nearby histidine residue (suggested by recent mutagenesis studies and crystallographic work) and, provided an electron source is available, leads to formation of an oxyl-complex after cleavage of the O-O bond and dissociation of water. The oxyl complex either reacts with the substrate or is further protonated to a hydroxyl complex. Both the oxyl and hydroxyl complexes are also readily generated from a reaction with H2O2. The C-H abstraction by the oxyl and hydroxy complexes is overall favorable with activation barriers of 69 and 94 kJ/mol, compared to the much higher barrier (156 kJ/mol) obtained for the copper-superoxo species. We obtain good structural agreement for intermediates for which structural data are available and the estimated reaction energies agree with experimental rate constants. Thus, our suggested mechanism is the most complete to date and concur with available experimental evidence.Comment: Comments added + a few additional calculations after revision for Chem. Sc

Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory

The combination of density functional theory (DFT) with a multiconfigurational wave function is an efficient way to include dynamical correlation in calculations with multiconfiguration self-consistent field wave functions. These methods can potentially be employed to elucidate reaction mechanisms in bio-inorganic chemistry, where many other methods become either too computationally expensive or too inaccurate. In this paper, a complete active space (CAS) short-range DFT (CAS-srDFT) hybrid was employed to investigate a bio-inorganic system, namely H2 binding to the active site of [NiFe] hydrogenase. This system was previously investigated with coupled-cluster (CC) and multiconfigurational methods in form of cumulant-approximated second-order perturbation theory, based on the density matrix renormalization group (DMRG). We find that it is more favorable for H2 to bind to Ni than to Fe, in agreement with previous CC and DMRG calculations. The accuracy of CAS-srDFT is comparable to both CC and DMRG, despite that much smaller active spaces were employed. This enhanced efficiency at smaller active spaces shows that CAS-srDFT can become a useful method for bio-inorganic chemistry.Comment: 22 page

Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes?

The lytic polysaccharide monooxygenase (LPMO) enzymes boost polysaccharide depolymerization through oxidative chemistry, which has fueled the hope for more energy-efficient production of biofuel. We have recently proposed a mechanism for the oxidation of the polysaccharide substrate (Hedeg{\aa}rd & Ryde, Chem. Sci. 2018, 9, 3866). In this mechanism, complexes with superoxide, oxyl, as well as hydroxyl (i.e. [CuO2]+, [CuO]+ and [CuOH]2+) cores were involved. These complexes can have both singlet and triplet spin states, and both spin-states may be important for how LPMOs function during catalytic turnover. Previous calculations on LPMOs have exclusively been based on density functional theory (DFT). However, different DFT functionals are known to display large differences for spin-state splittings in transition-metal complexes, and this has also been an issue for LPMOs. In this paper, we study the accuracy of DFT for spin-state splittings in superoxide, oxyl, and hydroxyl intermediates involved in LPMO turnover. As reference we employ multiconfigurational perturbation theory (CASPT2).Comment: 29 pages, 5 figures, 5 table

Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

We present here the coupling of a polarizable embedding (PE) model to the recently developed multiconfiguration short-range density functional theory method (MC-srDFT), which can treat multiconfigurational systems with a simultaneous account for dynamical and static correlation effects. PE-MC-srDFT is designed to combine efficient treatment of complicated electronic structures with inclusion of effects from the surrounding environment. The environmental effects encompass classical electrostatic interactions as well as polarization of both the quantum region and the environment. Using response theory, molecular properties such as excitation energies and oscillator strengths can be obtained. The PE-MC-srDFT method and the additional terms required for linear response have been implemented in a development version of DALTON. To benchmark the PE-MC-srDFT approach against the literature data, we have investigated the low-lying electronic excitations of acetone and uracil, both immersed in water solution. The PE-MC-srDFT results are consistent and accurate, both in terms of the calculated solvent shift and, unlike regular PE-MCSCF, also with respect to the individual absolute excitation energies. To demonstrate the capabilities of PE-MC-srDFT, we also investigated the retinylidene Schiff base chromophore embedded in the channelrhodopsin protein. While using a much more compact reference wave function in terms of active space, our PE-MC-srDFT approach yields excitation energies comparable in quality to CASSCF/CASPT2 benchmarks. (C) 2015 AIP Publishing LLC

Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks

Explicit embedding methods combined with the complex polarization propagator (CPP) enable the modeling of spectroscopy for increasingly complex systems with a high density of states. We present the first derivation and implementation of the CPP in four- and exact-two-component (X2C) polarizable embedding (PE) frameworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP, respectively. We illustrate the methods by estimating the solvent effect on ultraviolet-visible (UV-vis) and X-ray atomic absorption (XAS) spectra of [Rh(H2O)6]3+ and [Ir(H2O)6]3+ immersed in aqueous solution. We moreover estimate solvent effects on UV-vis spectra of a platinum complex that can be photochemically activated (in water) to kill cancer cells. Our results clearly show that the inclusion of the environment is required: UV-vis and (to a lesser degree) XAS spectra can become qualitatively different from vacuum calculations. Comparison of PE-4c-CPP and PE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect obtained with the 4c methods