QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study

Refining details of the structural and electronic properties of the CuB site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations

This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the Cu_B catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His³³, His¹³⁷, and His¹³⁹ on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the Cu_B site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the Cu_B center is an essential factor that makes it less efficient than the Cu_C site in the methane oxidation. Therefore, according to the Cu_B site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O₂ molecule prior to its activation must be necessary. This scenario is less likely to occur in the Cu_C center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.

Decoding the Ambiguous Electron Paramagnetic Resonance Signals in the Lytic Polysaccharide Monooxygenase from Photorhabdus luminescens

Understanding the structure and function of lytic polysaccharide monooxygenases (LPMOs), copper enzymes that degrade recalcitrant polysaccharides, requires the reliable atomistic interpretation of electron paramagnetic resonance (EPR) data on the Cu(II) active site. Among various LPMO families, the chitin-active PlAA10 shows an intriguing phenomenology with distinct EPR signals, a major rhombic and a minor axial signal. Here, we combine experimental and computational investigations to uncover the structural identity of these signals. X-band EPR spectra recorded at different pH values demonstrate pH-dependent population inversion: the major rhombic signal at pH 6.5 becomes minor at pH 8.5, where the axial signal dominates. This suggests that a protonation change is involved in the interconversion. Precise structural interpretations are pursued with quantum chemical calculations. Given that accurate calculations of Cu g-tensors remain challenging for quantum chemistry, we first address this problem via a thorough calibration study. This enables us to define a density functional that achieves accurate and reliable prediction of g-tensors, giving confidence in our evaluation of PlAA10 LPMO models. Large models were considered that include all parts of the protein matrix surrounding the Cu site, along with the characteristic second-sphere features of PlAA10. The results uniquely identify the rhombic signal with a five-coordinate Cu ion bearing two water molecules in addition to three N-donor ligands. The axial signal is attributed to a four-coordinate Cu ion where only one of the waters remains bound, as hydroxy. Alternatives that involve decoordination of the histidine brace amino group are unlikely based on energetics and spectroscopy. These results provide a reliable spectroscopy-consistent view on the plasticity of the resting state in PlAA10 LPMO as a foundation for further elucidating structure-property relationships and the formation of catalytically competent species. Our strategy is generally applicable to the study of EPR parameters of mononuclear copper-containing metalloenzymes.

Review on the QM/MM Methodologies and Their Application to Metalloproteins

The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.

EPR Spectroscopy of Cu(II) Complexes: Prediction of g-Tensors Using Double-Hybrid Density Functional Theory

Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for all chemical systems. Among transition metal ions, Cu(II) centers in inorganic chemistry and biology, and their associated EPR properties such as hyperfine coupling and g-tensors, pose exceptional difficulties for all levels of quantum chemistry. In the present work, we approach the problem of Cu(II) g-tensor calculations using double-hybrid density functional theory (DHDFT). Using a reference set of 18 structurally and spectroscopically characterized Cu(II) complexes, we evaluate a wide range of modern double-hybrid density functionals (DHDFs) that have not been applied previously to this problem. Our results suggest that the current generation of DHDFs consistently and systematically outperform other computational approaches. The B2GP-PLYP and PBE0-DH functionals are singled out as the best DHDFs on average for the prediction of Cu(II) g-tensors. The performance of the different functionals is discussed and suggestions are made for practical applications and future methodological developments.

Spiers Memorial Lecture: Activating Metal Sites for Biological Electron Transfer

Metal sites in biology often exhibit unique spectroscopic features that reflect novel geometric and electronic structures imposed by the protein that are key to reactivity. The Blue copper active site...

Converged Structural and Spectroscopic Properties for Refined QM/MM Models of Azurin

Blue copper proteins continue to challenge experiment and theory with their electronic structure and spectroscopic properties that respond sensitively to the coordination environment of the copper ion. In this work, we report state-of-the art electronic structure studies for geometric and spectroscopic properties of the archetypal "Type I" copper protein azurin in its Cu(II) state. A hybrid quantum mechanics/molecular mechanics (QM/MM) approach is used, employing both density functional theory (DFT) and coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) methods for the QM region, the latter method making use of the domain-based local pair natural orbital (DLPNO) approach. Models of increasing QM size are employed to investigate the convergence of critical geometric parameters. It is shown that convergence is slow and that a large QM region is critical for reproducing the short experimental Cu-SCys112 distance. The study of structural convergence is followed by investigation of spectroscopic parameters using both DFT and DLPNO-CC methods and comparing these to the experimental spectrum using simulations. The results allow us to examine for the first time the distribution of spin densities and hyperfine coupling constants at the coupled cluster level, leading us to revisit the experimental assignment of the 33S hyperfine splitting. The wavefunction-based approach to obtain spin-dependent properties of open-shell systems demonstrated here for the case of azurin is transferable and applicable to a large array of bioinorganic systems.

Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase

Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.

Comparison of Density Functional and Correlated Wave Function Methods for the Prediction of Cu(II) Hyperfine Coupling Constants

The reliable prediction of Cu(II) hyperfine coupling constants remains a challenge for quantum chemistry. Until recently only density functional theory (DFT) could target this property for systems of realistic size. However, wave function based methods become increasingly applicable. In the present work, we define a large set of Cu(II) complexes with experimentally known hyperfine coupling constants and use it to investigate the performance of modern quantum chemical methods for the prediction of this challenging spectroscopic parameter. DFT methods are evaluated against orbital‐optimized second‐order Møller‐Plesset (OO‐MP2) theory and coupled cluster calculations including singles and doubles excitations, driven by the domain‐based local pair natural orbital approach (DLPNO‐CCSD). Special attention is paid to the definition of a basis set that converges adequately toward the basis set limit for the given property for all methods considered in this study, and a specifically optimized basis set is proposed for this purpose. The results suggest that wave function based methods can supplant but do not outcompete DFT for the calculation of Cu(II) hyperfine coupling constants. Mainstream hybrid functionals such as B3PW91 remain on average the best choice.

Quantum Chemical Calculation of Molecular and Periodic Peptide and Protein Structures

Special-purpose classical force fields (FFs) provide good accuracy at very low computational cost, but their application is limited to systems for which potential energy functions are available. This excludes most metal-containing proteins or those containing cofactors. In contrast, the GFN2-xTB semiempirical quantum chemical method is parametrized for almost the entire periodic table. The accuracy of GFN2-xTB is assessed for protein structures with respect to experimental X-ray data. Furthermore, the results are compared with those of two special-purpose FFs, HF-3c, PM6-D3H4X, and PM7. The test sets include proteins without any prosthetic groups as well as metalloproteins. Crystal packing effects are examined for a set of smaller proteins to validate the molecular approach. For the proteins without prosthetic groups, the special purpose FF OPLS-2005 yields the smallest overall RMSD to the X-ray data but GFN2-xTB provides similarly good structures with even better bond-length distributions. For the metalloproteins with up to 5000 atoms, a good overall structural agreement is obtained with GFN2-xTB. The full geometry optimizations of protein structures with on average 1000 atoms in wall-times below 1 day establishes the GFN2-xTB method as a versatile tool for the computational treatment of various biomolecules with a good accuracy/computational cost ratio.

Conformational Analyses of Physiological Binary and Ternary Copper(II) Complexes with l-Asparagine and l-Histidine; Study of Tridentate Binding of Copper(II) in Aqueous Solution

This study explores the structural properties and energy landscapes of the physiologically important bis(l‐asparaginato)copper(II) [Cu(l‐Asn)₂] and (l‐histidinato)(l‐asparaginato)copper(II) [Cu(l‐His)(l‐Asn)]. The conformational analyses in the gas phase and implicitly modeled water medium, and magnetic parameters of electron paramagnetic resonance spectra were attained using density functional theory calculations. The apical Cu^II coordination and hydrogen bonding were analyzed. Predicted lower‐energy structures enabled the confirmation and, for apical bonding, also the refinement of structural proposals from literature. Available experimental results were indecisive regarding the amido‐group binding in the Cu^II equatorial plane in solutions, but the examination of the relative stability of Cu(l‐Asn)₂ conformers in 30 binding modes confirms the glycine‐like mode as the most stable one. Previously reported experimental results for Cu(l‐His)(l‐Asn) were interpreted for l‐His to have a tridentate histamine‐like mode. However, the aqueous conformers with l‐His in the glycinato mode are also predicted to have low energies, which does not contradict the tridentate l‐His binding. The predicted magnetic parameters of conformers with an apical oxygen atom (intramolecular or from a water molecule) can reproduce the experimental data. An extent of conformational flexibility and abundance of l‐His‐containing ternary copper(II) amino acid complexes under physiological conditions may be related.

Hypothesis: entaticversusecstatic states in metalloproteins

Biological metal sites are optimized for function by conformational properties of the protein macroligand.

Selected-Nuclei Method for the Computation of Hyperfine Coupling Constants within Second-Order Møller-Plesset Perturbation Theory

We introduce a new ansatz to compute hyperfine coupling constants of selected nuclei at the level of second-order Møller-Plesset perturbation (MP2) and double-hybrid density functional theory with reduced computational effort, opening the route to the analyis of hyperfine coupling constants of large molecular structures. Our approach is based on a reformulation of the canonical MP2 term in atomic orbitals, thus exploiting the locality of electron correlation. We show that a perturbation-including integral screening reduces the scaling behavior of the number of significant two-electron integrals to sublinear. This selected-nuclei approach allows for an efficient computation within scaled-opposite spin (SOS) RI-MP2 on massively parallelized architectures such as graphical processor units (GPUs), thus enabling studies on the influence of the environment on hyperfine coupling constants.

A General Route to Include Pauli Repulsion and Quantum Dispersion Effects in QM/MM Approaches

A methodology to account for nonelectrostatic interactions in Quantum Mechanical (QM)/Molecular Mechanics (MM) approaches is developed. Formulations for Pauli repulsion and dispersion energy, explicitly depending on the QM density, are derived. Such expressions are based on the definition of an auxiliary density on the MM portion and the Tkatchenko-Scheffler (TS) approach, respectively. The developed method is general enough to be applied to any QM/MM method and partition, provided an accurate tuning of a small number of parameters is obtained. The coupling of the method with both nonpolarizable and fully polarizable QM/fluctuating charge (FQ) approaches is reported and applied. A suitable parametrization for the aqueous solution, so that its most representative features are well reproduced, is outlined. Then, the obtained parametrization and method are applied to calculate the nonelectrostatic (repulsion and dispersion) interaction energy of nicotine in aqueous solution.

A QM/MM study of the nature of the entatic state in plastocyanin

Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory‐based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Asn47 and Phe114 modulate the inner sphere reorganization energies of type zero copper proteins

The geometric structures and electron transfer properties of type 1 Cu proteins are reasonably understood at the molecular level (E. I. Solomon and R. G. Hadt, Coord. Chem. Rev., 2011, 255, 774-789, J. J. Warren, K. M. Lancaster, J. H. Richards and H. B. Gray, J. Inorg. Biochem., 2012, 115, 119-126). Much understanding of type 1 copper electron transfer reactivity has come from site directed mutagenesis studies. For example, artificial "type zero" Cu-centres constructed in cupredoxin-azurin have showcased the capacity of outer-sphere hydrogen bonding networks to enhance Cu II/I electron transfer reactivity. In this paper, we have elaborated on earlier kinetics and electronic structural studies of type zero Cu by calculating the inner sphere reorganization energies of type 1, type 2, and type zero Cu proteins using density functional theory (DFT). Although the choice of density functionals for copper systems is not straightforward, we have benchmarked the density functionals against the recently reported ESI-PES data for two synthetic copper models (S. Niu, D.-L. Huang, P. D. Dau, H.-T. Liu, L.-S. Wang and T. J. Ichiye, Chem. Theory Comput., 2014, 10, 1283). For the Cu proteins, our calculations predict that changes in the coordination number upon metal reduction lead to large inner sphere reorganization energies for type 2 Cu sites, whereas retention in the coordination number is observed for type zero Cu sites. These variations in the coordination number are modulated by the outer-sphere coordinating residues Asn47 and Phe114, which are involved in hydrogen bonding with the Asp112 side chain.

Electronic Structure of a Cu(II)-Alkoxide Complex Modeling Intermediates in Copper-Catalyzed Alcohol Oxidations

In the copper-catalyzed oxidation of alcohols to aldehydes, a Cu(II)-alkoxide (Cu(II)-OR) intermediate is believed to modulate the αC-H bond strength of the deprotonated substrate to facilitate the oxidation. As a structural model for these intermediates, we characterized the electronic structure of the stable compound Tp(tBu)Cu(II)(OCH2CF3) (Tp(tBu) = hydro-tris(3-tert-butyl-pyrazolyl)borate) and investigated the influence of the trifluoroethoxide ligand on the electronic structure of the complex. The compound exhibits an electron paramagnetic resonance (EPR) spectrum with an unusually large gzz value of 2.44 and a small copper hyperfine coupling Azz of 40 × 10(-4) cm(-1) (120 MHz). Single-crystal electron nuclear double resonance (ENDOR) spectra show that the unpaired spin population is highly localized on the copper ion (≈68%), with no more than 15% on the ethoxide oxygen. Electronic absorption and magnetic circular dichroism (MCD) spectra show weak ligand-field transitions between 5000 and 12,000 cm(-1) and an intense ethoxide-to-copper charge transfer (LMCT) transition at 24,000 cm(-1), resulting in the red color of this complex. Resonance Raman (rR) spectroscopy reveals a Cu-O stretch mode at 592 cm(-1). Quantum chemical calculations support the interpretation and assignment of the experimental data. Compared to known Cu(II)-thiolate and Cu(II)-alkylperoxo complexes from the literature, we found an increased σ interaction in the Cu(II)-OR bond that results in the spectroscopic features. These insights lay the basis for further elucidating the mechanism of copper-catalyzed alcohol oxidations.

Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges

A polarizable quantum mechanics (QM)/ molecular mechanics (MM) approach recently developed for Hartree-Fock (HF) and Kohn-Sham (KS) methods has been extended to energies and analytical gradients for MP2, double hybrid functionals, and TD-DFT models, thus allowing the computation of equilibrium structures for excited electronic states together with more accurate results for ground electronic states. After a detailed presentation of the theoretical background and of some implementation details, a number of test cases are analyzed to show that the polarizable embedding model based on fluctuating charges (FQ) is remarkably more accurate than the corresponding electronic embedding based on a fixed charge (FX) description. In particular, a set of electronegativities and hardnesses has been optimized for interactions between QM and FQ regions together with new repulsion-dispersion parameters. After validation of both the numerical implementation and of the new parameters, absorption electronic spectra have been computed for representative model systems including vibronic effects. The results show remarkable agreement with full QM computations and significant improvement with respect to the corresponding FX results. The last part of the article provides some hints about computation of solvatochromic effects on absorption spectra in aqueous solution as a function of the number of FQ water molecules and on the use of FX external shells to improve the convergence of the results. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Structural differences between the active sites of the Ni-A and Ni-B states of the [NiFe] hydrogenase: an approach by quantum chemistry and single crystal ENDOR spectroscopy

The two resting forms of the active site of [NiFe] hydrogenase, Ni-A and Ni-B, have significantly different activation kinetics, but reveal nearly identical spectroscopic features which suggest the two states exhibit subtle structural differences. Previous studies have indicated that the states differ by the identity of the bridging ligand between Ni and Fe; proposals include OH(-), OOH(-), H2O, O(2-), accompanied by modified cysteine residues. In this study, we use single crystal ENDOR spectroscopy and quantum chemical calculations within the framework of density functional theory (DFT) to calculate vibrational frequencies, (1)H and (17)O hyperfine coupling constants and g values with the aim to compare these data to experimental results obtained by crystallography, FTIR and EPR/ENDOR spectroscopy. We find that the Ni-A and Ni-B states are constitutional isomers that differ in their fine structural details. Calculated vibrational frequencies for the cyano and carbonyl ligands and (1)H and (17)O hyperfine coupling constants indicate that the bridging ligand in both Ni-A and Ni-B is indeed an OH(-) ligand. The difference in the isotropic hyperfine coupling constants of the β-CH2 protons of Cys-549 is sensitive to the orientation of Cys-549; a difference of 0.5 MHz is observed experimentally for Ni-A and 1.9 MHz for Ni-B, which results from a rotation of 7 degrees about the Cα-Cβ-Sγ-Ni dihedral angle. Likewise, the difference of the intermediate g value is correlated with a rotation of Cys-546 of about 10 degrees.

Dye chemistry with time-dependent density functional theory

In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.

The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.

Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control

Cupredoxins perform copper-mediated long-range electron transfer (ET) in biological systems. Their copper-binding sites have evolved to force copper ions into ET-competent systems with decreased reorganization energy, increased reduction potential, and a distinct electronic structure compared with those of non-ET-competent copper complexes. The entatic or rack-induced state hypothesis explains these special properties in terms of the strain that the protein matrix exerts on the metal ions. This idea is supported by X-ray structures of apocupredoxins displaying "closed" arrangements of the copper ligands like those observed in the holoproteins; however, it implies completely buried copper-binding atoms, conflicting with the notion that they must be exposed for copper loading. On the other hand, a recent work based on NMR showed that the copper-binding regions of apocupredoxins are flexible in solution. We have explored five cupredoxins in their "closed" apo forms through molecular dynamics simulations. We observed that prearranged ligand conformations are not stable as the X-ray data suggest, although they do form part of the dynamic landscape of the apoproteins. This translates into variable flexibility of the copper-binding regions within a rigid fold, accompanied by fluctuations of the hydrogen bonds around the copper ligands. Major conformations with solvent-exposed copper-binding atoms could allow initial binding of the copper ions. An eventual subsequent incursion to the closed state would result in binding of the remaining ligands, trapping the closed conformation thanks to the additional binding energy and the fastening of noncovalent interactions that make up the rack.

Pulsed electron paramagnetic resonance spectroscopy of (33)S-labeled molybdenum cofactor in catalytically active bioengineered sulfite oxidase

Molybdenum enzymes contain at least one pyranopterin dithiolate (molybdopterin, MPT) moiety that coordinates Mo through two dithiolate (dithiolene) sulfur atoms. For sulfite oxidase (SO), hyperfine interactions (hfi) and nuclear quadrupole interactions (nqi) of magnetic nuclei (I ≠ 0) near the Mo(V) (d(1)) center have been measured using high-resolution pulsed electron paramagnetic resonance (EPR) methods and interpreted with the help of density functional theory (DFT) calculations. These have provided important insights about the active site structure and the reaction mechanism of the enzyme. However, it has not been possible to use EPR to probe the dithiolene sulfurs directly since naturally abundant (32)S has no nuclear spin (I = 0). Here we describe direct incorporation of (33)S (I = 3/2), the only stable magnetic sulfur isotope, into MPT using controlled in vitro synthesis with purified proteins. The electron spin echo envelope modulation (ESEEM) spectra from (33)S-labeled MPT in this catalytically active SO variant are dominated by the "interdoublet" transition arising from the strong nuclear quadrupole interaction, as also occurs for the (33)S-labeled exchangeable equatorial sulfite ligand [ Klein, E. L., et al. Inorg. Chem. 2012 , 51 , 1408 - 1418 ]. The estimated experimental hfi and nqi parameters for (33)S (aiso = 3 MHz and e(2)Qq/h = 25 MHz) are in good agreement with those predicted by DFT. In addition, the DFT calculations show that the two (33)S atoms are indistinguishable by EPR and reveal a strong intermixing between their out-of-plane pz orbitals and the dxy orbital of Mo(V).

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Computational study of the structure and electronic circular dichroism spectroscopy of blue copper proteins

The calculation of the electronic circular dichroism (CD) spectra of the oxidized form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated. Excitation energies and transition strengths are computed using multireference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimized in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures, it is shown that the intensity of this band is sensitive to the nonplanarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.

Outer-sphere contributions to the electronic structure of type zero copper proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called "type zero" sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding.

Identity of the exchangeable sulfur-containing ligand at the Mo(V) center of R160Q human sulfite oxidase

In our previous study of the fatal R160Q mutant of human sulfite oxidase (hSO) at low pH (Astashkin et al. J. Am. Chem. Soc.2008, 130, 8471-8480), a new Mo(V) species, denoted "species 1", was observed at low pH values. Species 1 was ascribed to a six-coordinate Mo(V) center with an exchangeable terminal oxo ligand and an equatorial sulfate group on the basis of pulsed EPR spectroscopy and (33)S and (17)O labeling. Here we report new results for species 1 of R160Q, based on substitution of the sulfur-containing ligand by a phosphate group, pulsed EPR spectroscopy in K(a)- and W-bands, and extensive density functional theory (DFT) calculations applied to large, more realistic molecular models of the enzyme active site. The combined results unambiguously show that species 1 has an equatorial sulfite as the only exchangeable ligand. The two types of (17)O signals that are observed arise from the coordinated and remote oxygen atoms of the sulfite ligand. A typical five-coordinate Mo(V) site is compatible with the observed and calculated EPR parameters.