51V NMR chemical shifts from quantum-mechanical/molecular-mechanical models of vanadium bromoperoxidase

According to quantum-mechanical/molecular-mechanical (QM/MM) optimizations, the active-site geometries of vanadium-dependent bromoperoxidase (VBPO) and vanadium-dependent chloroperoxidase (VCPO) are very similar. 51V NMR chemical shifts calculated from QM/MM-optimized models of VBPO are critically compared to VCPO and are found to be very similar for the two related proteins. The primary difference between these related structures, the presence of a His411 in VBPO whereas Phe397 is located at that position in VCPO, is studied via analysis of the respective theoretical 51V NMR spectra. The long-range electrostatic effects from more distal residues are also studied to establish their effect. Similar results are obtained for the two active sites of the VBPO homodimer. The experimentally observed shielding of the isotropic 51V NMR chemical shift on going from VCPO to VBPO is somewhat underestimated in the QM/MM models studied. NMR and NQC tensors of both enzymes are predicted to show noticeable differences, suggesting that precise solid-state 51V NMR data, when they become available, can be a sensitive probe for subtle differences in structural details between these enzymes.     

51V solid-state magic angle spinning NMR spectroscopy and DFT studies of oxovanadium(V) complexes mimicking the active site of vanadium haloperoxidases

A series of 11 oxovanadium(V) complexes mimicking the active site of vanadium haloperoxidases have been investigated by (51)V magic angle spinning NMR spectroscopy and density functional theory (DFT). The MAS spectra are dominated by the anisotropic quadrupolar and chemical shielding interactions; for these compounds, C(Q) ranges from 3 to 8 MHz, and delta(sigma) is in the range 340-730 ppm. The quadrupolar coupling and chemical shielding tensors as well as their relative orientations have been determined by numerical simulations of the spectra. The spectroscopic NMR observables appear to be very sensitive to the details of the electronic and geometric environment of the vanadium center in these complexes. For the four crystallographically characterized compounds from the series, the quadrupolar and chemical shielding anisotropies were computed at the DFT level using two different basis sets, and the calculated tensors were in general agreement with the experimental solid-state NMR data. A combination of (51)V solid-state NMR and computational methods is thus beneficial for investigation of the electrostatic and geometric environment in diamagnetic vanadium systems with moderate quadrupolar anisotropies.     

Characterization of noninnocent metal complexes using solid-state NMR spectroscopy: o-dioxolene vanadium complexes

(51)V solid-state NMR (SSNMR) studies of a series of noninnocent vanadium(V) catechol complexes have been conducted to evaluate the possibility that (51)V NMR observables, quadrupolar and chemical shift anisotropies, and electronic structures of such compounds can be used to characterize these compounds. The vanadium(V) catechol complexes described in these studies have relatively small quadrupolar coupling constants, which cover a surprisingly small range from 3.4 to 4.2 MHz. On the other hand, isotropic (51)V NMR chemical shifts cover a wide range from -200 to 400 ppm in solution and from -219 to 530 ppm in the solid state. A linear correlation of (51)V NMR isotropic solution and solid-state chemical shifts of complexes containing noninnocent ligands is observed. These experimental results provide the information needed for the application of (51)V SSNMR spectroscopy in characterizing the electronic properties of a wide variety of vanadium-containing systems and, in particular, those containing noninnocent ligands and that have chemical shifts outside the populated range of -300 to -700 ppm. The studies presented in this report demonstrate that the small quadrupolar couplings covering a narrow range of values reflect the symmetric electronic charge distribution, which is also similar across these complexes. These quadrupolar interaction parameters alone are not sufficient to capture the rich electronic structure of these complexes. In contrast, the chemical shift anisotropy tensor elements accessible from (51)V SSNMR experiments are a highly sensitive probe of subtle differences in electronic distribution and orbital occupancy in these compounds. Quantum chemical (density functional theory) calculations of NMR parameters for [VO(hshed)(Cat)] yield a (51)V chemical shift anisotropy tensor in reasonable agreement with the experimental results, but surprisingly the calculated quadrupolar coupling constant is significantly greater than the experimental value. The studies demonstrate that substitution of the catechol ligand with electron-donating groups results in an increase in the HOMO-LUMO gap and can be directly followed by an upfield shift for the vanadium catechol complex. In contrast, substitution of the catechol ligand with electron-withdrawing groups results in a decrease in the HOMO-LUMO gap and can directly be followed by a downfield shift for the complex. The vanadium catechol complexes were used in this work because (51)V is a half-integer quadrupolar nucleus whose NMR observables are highly sensitive to the local environment. However, the results are general and could be extended to other redox-active complexes that exhibit coordination chemistry similar to that of the vanadium catechol complexes.     

Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants

We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.     

Residue ionization in LpxC directly observed by 67Zn NMR spectroscopy

The pH dependence of the solid-state (67)Zn NMR lineshapes has been measured for both the wild type (WT) and the H265A mutant of Aquifex aeolicus LpxC, each in the absence of substrate (resting state). The (67)Zn NMR spectrum of WT LpxC at pH 6 (prepared at 0 degrees C) contains two overlapping quadrupole lineshapes with C q values of 10 and 12.9 MHz, while the spectrum measured for the sample prepared at a pH near 9 (at 0 degrees C) is dominated by the appearance of a third species with a C q of 14.3 MHz. These findings are consistent with the two p K a values previously observed by the bell-shaped dependence of the LpxC-catalyzed reaction. On the basis of comparison of the experimental results with predictions from quantum mechanical/molecular mechanical (QM/MM) modeling, we suggest that p K a1 (low pH) represents the ionization of Glu78 and p K a2 (high pH) reflects the ionization of another active site residue located near the zinc ion, such as His265. These results are also consistent with water being bound to the Zn (2+) ion throughout this pH range. The (67)Zn NMR spectra of the H265A mutant appear to be pH independent, with a C q of 9.55 MHz being sufficient to describe both low- and high-pH data. The QM/MM models of the H265A mutant suggest that over this pH range water is bound to the zinc ion while Glu78 is protonated.     

(51)V NMR parameters of VOCl(3): static and dynamic density functional study from the gas phase to the bulk

(51)V NMR parameters have been calculated for VOCl(3), the reference compound in (51)V NMR spectroscopy, in order to capture environmental effects in both the neat liquid and the solid state. Using a combination of periodic geometry optimizations and Car-Parrinello molecular dynamics simulations with embedded cluster NMR calculations, we are able to test the ability of current computational approaches to reproduce (51)V NMR properties (isotropic shifts, anisotropic shifts and quadrupole coupling constants) in the gas, liquid and solid states, for direct comparison with liquid and solid-state experimental data. The results suggest that environmental effects in the condensed phases can be well captured by an embedded cluster approach and that the remaining discrepancy with experiment may be due to the approximate density functionals in current use. The predicted gas-to-liquid shift on the isotropic shielding constant is small, validating the common practice to use a single VOCl(3), molecule as reference in (51)V NMR computations.     

Oxoperoxo vanadium(V) complexes of L-lactic acid: density functional theory study of structure and NMR chemical shifts

Various combinations of density functionals and pseudopotentials with associated valence basis-sets are compared for reproducing the known solid-state structure of [V 2O 2(OO) 2 l-lact 2] (2-) cis . Gas-phase optimizations at the B3LYP/SBKJC level have been found to provide a structure that is close to that seen in the solid state by X-ray diffraction. Although this may result in part from error compensation, this optimized structure allowed satisfactory reproduction of solution multinuclear NMR chemical shifts of the complex in all-electron DFT-IGLO calculations (UDFT-IGLO-PW91 level), suggesting that it is probably close to that found in solution. This combination of approaches has subsequently been used to optimize the structures of the vanadium oxoperoxo complexes [V 2O 3(OO) l-lact 2] (2-) cis , [V 2O 3(OO) l-lact 2] (2-) trans , and [VO(OO)( l-lact)(H 2O)] (-) cis . The (1)H, (13)C, (51)V, and (17)O NMR chemical shifts for these complexes have been calculated and compared with the experimental solution chemical shifts. Excellent agreement is seen with the (13)C chemical shifts, while somewhat inferior agreement is found for (1)H shifts. The (51)V and (17)O chemical shifts of the dioxo vanadium centers are well reproduced, with differences between theoretical and experimental shifts ranging from 22.9 to 35.6 ppm and from 25.1 to 43.7 ppm, respectively. Inferior agreement is found for oxoperoxo vanadium centers, with differences varying from 137.3 to 175.0 ppm for (51)V shifts and from 148.7 to 167.0 ppm for (17)O(oxo) shifts. The larger errors are likely to be due to overestimated peroxo O-O distances. The chosen methodology is able to predict and analyze a number of interesting structural features for vanadium(V) oxoperoxocomplexes of alpha-hydroxycarboxylic acids.     

Isocyanide in Biochemistry? A Theoretical Investigation of the Electronic Effects and Energetics of Cyanide Ligand Protonation in [FeFe]‐Hydrogenases

The presence of Fe‐bound cyanide ligands in the active site of the proton‐reducing enzymes [FeFe]‐hydrogenases has led to the hypothesis that such Brønsted–Lowry bases could be protonated during the catalytic cycle, thus implying that hydrogen isocyanide (HNC) might have a relevant role in such crucial microbial metabolic paths. We present a hybrid quantum mechanical/molecular mechanical (QM/MM) study of the energetics of CN^? protonation in the enzyme, and of the effects that cyanide protonation can have on [FeFe]‐hydrogenase active sites. A detailed analysis of the electronic properties of the models and of the energy profile associated with H₂ evolution clearly shows that such protonation is dysfunctional for the catalytic process. However, the inclusion of the protein matrix surrounding the active site in our QM/MM models allowed us to demonstrate that the amino acid environment was finely selected through evolution, specifically to lower the Brønsted–Lowry basicity of the cyanide ligands. In fact, the conserved hydrogen‐bonding network formed by these ligands and the neighboring amino acid residues is able to impede CN^? protonation, as shown by the fact that the isocyanide forms of [FeFe]‐hydrogenases do not correspond to stationary points on the enzyme QM/MM potential‐energy surface.     

51V magic angle spinning NMR spectroscopy of six-coordinate Lindqvist oxoanions: a sensitive probe for the electronic environment in vanadium-containing polyoxometalates. Counterions dictate the 51V fine structure constants in polyoxometalate solids

Geometric and electronic environments of vanadium have been addressed by (51)V magic angle spinning NMR spectroscopy of six-coordinated polyoxometalate solids. (C(4)H(9))(4)N(+) and mixed Na(+)/Cs(+) salts of the Lindqvist-type mono- and divanadium-substituted oxotungstates, [VW(5)O(19)](3-) and [V(2)W(4)O(19)](4-), have been prepared as microcrystalline and crystalline solids. The solid-state NMR spectra reflect the details of the local environment of the vanadium site in these hexametalate solids via the anisotropic quadrupolar and chemical shielding interactions. Remarkably, these (51)V fine structure constants in the solid state are dictated by the nature and geometry of the countercations. Electrostatic calculations of the electric field gradients at the vanadium atoms have been performed. Experimental trends are well reproduced with the simple electrostatic model, and explain the sensitivity of the anisotropic NMR parameters to the changes in the cationic environment at the vanadium site.     

Common system setup for the entire catalytic cycle of cytochrome P450(cam) in quantum mechanical/molecular mechanical studies

We describe a system setup that is applicable to all species in the catalytic cycle of cytochrome P450(cam). The chosen procedure starts from the X-ray coordinates of the ferrous dioxygen complex and follows a protocol that includes the careful assignment of protonation states, comparison between different conceivable hydration schemes, and system preparation through a series of classical minimizations and molecular dynamics (MD) simulations. The resulting setup was validated by quantum mechanical/molecular mechanical (QM/MM) calculations on the resting state, the pentacoordinated ferric and ferrous complexes, Compound I, the transition state and hydroxo intermediate of the C--H hydroxylation reaction, and the product complex. The present QM/MM results are generally consistent with those obtained previously with individual setups. Concerning hydration, we find that saturating the protein interior with water is detrimental and leads to higher structural flexibility and catalytically inefficient active-site geometries. The MD simulations favor a low water density around Asp251 that facilitates side chain rotation of protonated Asp251 during the conversion of Compound 0 to Compound I. The QM/MM results for the two preferred hydration schemes (labeled SE-1 and SE-4) are similar, indicating that slight differences in the solvation close to the active site are not critical as long as camphor and the crystallographic water molecules preserve their positions in the experimental X-ray structures.     

Investigating the vanadium environments in hydroxylamido V(V) dipicolinate complexes using 51V NMR spectroscopy and density functional theory

Using (51)V magic angle spinning solid-state NMR, SSNMR, spectroscopy and quantum chemical DFT calculations we have characterized the chemical shift and quadrupolar coupling parameters of a series of eight hydroxylamido vanadium(V) dipicolinate complexes of the general formula VO(dipic)(ONR1R2)(H2O) where R1 and R2 can be H, CH3, or CH2CH3. This class of vanadium compounds was chosen for investigation because of their seven-coordinate vanadium atom, a geometry for which there is limited (51)V SSNMR data. Furthermore, a systematic series of compounds with different electronic properties are available and allows for the effects of ligand substitution on the NMR parameters to be studied. The quadrupolar coupling constants, C(Q), are small, 3.0-3.9 MHz, but exhibit variations as a function of the ligand substitution. The chemical shift tensors in the solid state are sensitive to changes in both the hydroxylamide substituent and the dipic ligand, a sensitivity which is not observed for isotropic chemical shifts in solution. The chemical shift tensors span approximately 1000 ppm and are nearly axially symmetric. On the basis of DFT calculations of the chemical shift tensors, one of the largest contributors to the magnetic shielding anisotropy is an occupied molecular orbital with significant vanadium d(z)2 character along the V=O bond.     

NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study

We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.     

51V magic angle spinning NMR spectroscopy of Keggin anions [PVnW12-nO40](3+n)-: effect of countercation and vanadium substitution on fine structure constants

Vanadium environments in Keggin oxopolytungstates were characterized by (51)V solid-state MAS NMR spectroscopy. (C(4)H(9))(4)N(+)-, K(+)-, Cs(+)-, as well as mixed Na(+)/Cs(+)- salts of the mono-, di-, and trivanadium substituted oxotungstates, [VW(11)O(40)](4-), [V(2)W(10)O(40)](5-), and [V(3)W(9)O(40)](6-), have been prepared as microcrystalline and crystalline solids. Solid-state NMR spectra report on the local environment of the vanadium site in these Keggin ions via their anisotropic quadrupolar and chemical-shielding interactions. These (51)V fine structure constants in the solid state are determined by the number of vanadium atoms present in the oxoanion core. Surprisingly, the quadrupolar anisotropy tensors do not depend to any significant extent on the nature of the countercations. On the other hand, the chemical-shielding anisotropy tensors, as well as the isotropic chemical shifts, display large variations as a function of the cationic environment. This information can be used as a probe of the local cationic environment in the vanadium-substituted Keggin solids.     

QM/MM studies of Ni-Fe hydrogenases: the effect of enzyme environment on the structure and energies of the inactive and active states

The catalytically active (Ni-SI and Ni-R) and inactive states (Ni-A and Ni-B) of Ni-Fe hydrogenases have been studied using density functional theory (DFT) methods. Both isolated clusters and clusters embedded in the enzyme have been used to model the Ni-A, Ni-B, Ni-SI and Ni-R states. The BP86 and B3LYP functionals were employed, and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods were used for the embedded calculations. The QM/MM studies, rather than the isolated cluster calculations, were generally found to give structures which correlated better with X-ray data. The structure of the unready state (Ni-A), was correctly predicted by the QM/MM, but not by the isolated cluster calculation. Comparison with the observed crystal structure favoured the catalytically active state, Ni-SI, to be the protonated (Ni-SI(II)), rather than the unprotonated state (Ni-SI(I)). In the QM/MM studies, the binding of H(2) to Ni-SI(II) is preferred at the Ni (Ni-R(Ni)), rather than at the Fe centre (Ni-R(Fe)), in agreement with xenon binding studies, and in contrast to isolated cluster studies. These calculations cannot say with certainty which functional should be favoured, nor the preferred spin state of the catalytically active species. However, the lack of any predicted structure in which H(2) binds to the Fe centre, does favour a low spin state for Ni-SI(II), and the use of the BP86 functional. This is in agreement with recent high level ab initio calculations of a model of the Ni-SI(I) state.     

YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model

A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.     

Characterizing the protonation states of the catalytic residues in apo and substrate-bound human T-cell leukemia virus type 1 protease

Human T-cell leukemia virus type 1 (HTLV-1) protease is an attractive target when developing inhibitors to treat HTLV-1 associated diseases. To study the catalytic mechanism and design novel HTLV-1 protease inhibitors, the protonation states of the two catalytic aspartic acid residues must be determined. Free energy simulations have been conducted to study the proton transfer reaction between the catalytic residues of HTLV-1 protease using a combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulation. The free energy profiles for the reaction in the apo-enzyme and in an enzyme – substrate complex have been obtained. In the apo-enzyme, the two catalytic residues are chemically equivalent and are expected to be both unprotonated. Upon substrate binding, the catalytic residues of HTLV-1 protease evolve to a singly protonated state, in which the OD1 of Asp32 is protonated and forms a hydrogen bond with the OD1 of Asp32′, which is unprotonated. The HTLV-1 protease–substrate complex structure obtained from this simulation can serve as the Michaelis complex structure for further mechanistic studies of HTLV-1 protease while providing a receptor structure with the correct protonation states for the active site residues toward the design of novel HTLV-1 protease inhibitors through virtual screening.     

X-ray and NMR crystallography in an enzyme active site: the indoline quinonoid intermediate in tryptophan synthase

Chemical-level details such as protonation and hybridization state are critical for understanding enzyme mechanism and function. Even at high resolution, these details are difficult to determine by X-ray crystallography alone. The chemical shift in NMR spectroscopy, however, is an extremely sensitive probe of the chemical environment, making solid-state NMR spectroscopy and X-ray crystallography a powerful combination for defining chemically detailed three-dimensional structures. Here we adopted this combined approach to determine the chemically rich crystal structure of the indoline quinonoid intermediate in the pyridoxal-5'-phosphate-dependent enzyme tryptophan synthase under conditions of active catalysis. Models of the active site were developed using a synergistic approach in which the structure of this reactive substrate analogue was optimized using ab initio computational chemistry in the presence of side-chain residues fixed at their crystallographically determined coordinates. Various models of charge and protonation state for the substrate and nearby catalytic residues could be uniquely distinguished by their calculated effects on the chemical shifts measured at specifically (13)C- and (15)N-labeled positions on the substrate. Our model suggests the importance of an equilibrium between tautomeric forms of the substrate, with the protonation state of the major isomer directing the next catalytic step.     

Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor

The hydrogen abstraction reaction of camphor in cytochrome P450(cam) has been investigated in the native enzyme environment by combined quantum mechanical/molecular mechanical (QM/MM) calculations and in the gas phase by density functional calculations. This work has been motivated by contradictory published QM/MM results. In an attempt to pinpoint the origin of these discrepancies, we have systematically studied the factors that may affect the computed barriers, including the QM/MM setup, the optimization procedures, and the choice of QM region, basis set, and protonation states. It is found that the ChemShell and QSite programs used in the published QM/MM calculations yield similar results at given geometries, and that the discrepancies mainly arise from two technical issues (optimization protocols and initial system preparation) that need to be well controlled in QM/MM work. In the course of these systematic investigations, new mechanistic insights have been gained. The crystallographic water 903 placed near the oxo atom of Compound I lowers the hydrogen abstraction barrier by ca. 4 kcal/mol, and thus acts as a catalyst for this reaction. Spin density may appear at the A-propionate side chain of the heme if the carboxylate group is not properly screened, which might be expected to happen during protein dynamics, but not in static equilibrium situations. There is no clear correlation between the computed A-propionate spin density and the hydrogen abstraction barrier, and hence, no support for a previously proposed side-chain mediated transition state stabilization mechanism. Standard QM/MM optimizations yield an A-propionate environment close to the X-ray structure only for protonated Asp297, and not for deprotonated Asp297, but the computed barriers are similar in both cases. An X-ray like A-propionate environment can also be obtained when deprotonated Asp297 is included in the QM region and His355 is singly protonated, but this Compound II-type species with a closed-shell porphyrin ring has a higher hydrogen abstraction barrier and should thus not be mechanistically relevant.