Six popular density functionals in conjunction with the conductor-like screening (COSMO) solvation model have been used to obtain linear Mössbauer isomer shift (IS) and quadrupole splitting (QS) parameters for a test set of 20 complexes (with 24 sites) comprised of nonheme nitrosyls (Fe–NO) and non-nitrosyl (Fe–S) complexes. For the first time in an IS analysis, the Fe electron density was calculated both directly at the nucleus, ρ(0)N, which is the typical procedure, and on a small sphere surrounding the nucleus, ρ(0)S, which is the new standard algorithm implemented in the ADF software package. We find that both methods yield (near) identical slopes from each linear regression analysis but are shifted with respect to ρ(0) along the x-axis. Therefore, the calculation of the Fe electron density with either method gives calibration fits with equal predictive value. Calibration parameters obtained from the complete test set for OLYP, OPBE, PW91, and BP86 yield correlation coefficients (r2) of approximately 0.90, indicating that the calibration fit is of good quality. However, fits obtained from B3LYP and B3LYP* with both Slater-type and Gaussian-type orbitals are generally found to be of poorer quality. For several of the complexes examined in this study, we find that B3LYP and B3LYP* give geometries that possess significantly larger deviations from the experimental structures than OLYP, OPBE, PW91 or BP86. This phenomenon is particularly true for the di- and tetranuclear Fe complexes examined in this study. Previous Mössbauer calibration fit studies using these functionals have usually included mononuclear Fe complexes alone, where these discrepancies are less pronounced. An examination of spin expectation values reveals B3LYP and B3LYP* approach the weak-coupling limit more closely than the GGA exchange-correlation functionals. The high degree of variability in our calculated S2 values for the Fe–NO complexes highlights their challenging electronic structure. Significant improvements to the isomer shift calibrations are obtained for B3LYP and B3LYP* when geometries obtained with the OLYP functional are used. In addition, greatly improved performance of these functionals is found if the complete test set is grouped separately into Fe–NO and Fe–S complexes. Calibration fits including only Fe–NO complexes are found to be excellent, while those containing the non-nitrosyl Fe–S complexes alone are found to demonstrate less accurate correlations. Similar trends are also found with OLYP, OPBE, PW91, and BP86. Correlations between experimental and calculated QSs were also investigated. Generally, universal and separate Fe–NO and Fe–S fit parameters obtained to determine QSs are found to be of good to excellent quality for every density functional examined, especially if [Fe4(NO)4(μ3-S)4]− is removed from the test set.

Vitamin B(12) and its biologically active counterparts possess the only examples of carbon-cobalt bonds in living systems. The role of such motifs as radical reservoirs has potential application in future catalytic and electronic nanodevices. To fully understand radical generation in coenzyme B(12) (dAdoCbl)-dependent enzymes, however, major obstacles still need to be overcome. In this work, we have used Car-Parrinello molecular dynamics (CPMD) simulations, in a mixed quantum mechanics/molecular mechanics (QM/MM) framework, to investigate the initial stages of the methylmalonyl-CoA-mutase-catalyzed reaction. We demonstrate that the 5'-deoxyadenosyl radical (dAdo(•)) exists as a distinct entity in this reaction, consistent with the results of extensive experimental and some previous theoretical studies. We report free energy calculations and first-principles trajectories that help understand how B(12) enzymes catalyze coenzyme activation and control highly reactive radical intermediates.

We present a series of QM/MM calculations aimed at understanding the mechanism of the biological dehydration of glycerol. Strikingly and unusually, this process is catalyzed by two different radical enzymes, one of which is a coenzyme-B-dependent enzyme and the other which is a coenzyme-B-independent enzyme. We show that glycerol dehydration in the presence of the coenzyme-B-dependent enzyme proceeds via a 1,2-OH shift, which benefits from a significant catalytic reduction in the barrier. In contrast, the same reaction in the presence of the coenzyme-B-independent enzyme is unlikely to involve the 1,2-OH shift; instead, a strong preference for direct loss of water from a radical intermediate is indicated. We show that this preference, and ultimately the evolution of such enzymes, is strongly linked with the reactivities of the species responsible for abstracting a hydrogen atom from the substrate. It appears that the hydrogen-reabstraction step involving the product-related radical is fundamental to the mechanistic preference. The unconventional 1,2-OH shift seems to be required to generate a product-related radical of sufficient reactivity to cleave the relatively inactive C-H bond arising from the B cofactor. In the absence of B, it is the relatively weak S-H bond of a cysteine residue that must be homolyzed. Such a transformation is much less demanding, and its inclusion apparently enables a simpler overall dehydration mechanism.

With current therapies becoming less efficacious due to increased drug resistance, new inhibitors of both bacterial and malarial targets are desperately needed. The recently discovered methylerythritol phosphate (MEP) pathway for isoprenoid synthesis provides novel targets for the development of such drugs. Particular attention has focused on the IspH protein, the final enzyme in the MEP pathway, which uses its [4Fe–4S] cluster to catalyze the formation of the isoprenoid precursors IPP and DMAPP from HMBPP. IspH catalysis is achieved via a 2e–/2H+ reductive dehydroxylation of HMBPP; the mechanism by which catalysis is achieved, however, is highly controversial. The work presented herein provides the first step in assessing different routes to catalysis by using computational methods. By performing broken-symmetry density functional theory (BS–DFT) calculations that employ both the conductor-like screening solvation model (DFT/COSMO) and a finite-difference Poisson–Boltzmann self-consistent reaction field methodology (DFT/SCRF), we evaluate geometries, energies, and Mössbauer signatures of the different protonation states that may exist in the oxidized state of the IspH catalytic cycle. From DFT/SCRF computations performed on the oxidized state, we find a state where the substrate, HMBPP, coordinates the apical iron in the [4Fe–4S] cluster as an alcohol group (ROH) to be one of two, isoenergetic, lowest-energy states. In this state, the HMBPP pyrophosphate moiety and an adjacent glutamate residue (E126) are both fully deprotonated, making the active site highly anionic. Our findings that this low-energy state also matches the experimental geometry of the active site and that its computed isomer shifts agree with experiment validate the use of the DFT/SCRF method to assess relative energies along the IspH reaction pathway. Additional studies of IspH catalytic intermediates are currently being pursued.