Theoretical modeling of the nonenzymatic solvolysis of CMP-NeuAc in an acidic environment

A density-functional-theory investigation of the nonenzymatic solvolysis of the cytydine 5′-monophosphate N-acetylneuraminic acid and its derivatives in the acidic environment is presented. The theoretical calculations of the second stage of the reaction mechanism are in agreement with the hypothesis of a dissociative oxocarbenium-like transition state with proton transfer as a key part of the reaction. The geometries of the transition states of the reactions yielding -methyl and β-methyl glycosides are essentially different. This study provides new theoretical data that can be helpful in elucidating the mechanism of the carbohydrates hydrolysis as well as other reactions catalyzed by the glycosyltransferases.     

Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase

Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.     

Class I ribonucleotide reductase revisited: the effect of removing a proton on Glu441

The substrate mechanism of class I ribonucleotide reductase has been revisited using the hybrid density functional B3LYP method. The molecular model used is based on the X-ray structure and includes all the residues of the R1 subunit commonly considered in the RNR substrate conversion scheme: Cys439 initiating the reaction as a thiyl radical, the redox-active cysteines Cys225 and Cys462, and the catalytically important Glu441 and Asn437. In contrast to previous theoretical studies of the overall mechanism, Glu441 is added as an anion. All relevant transition states have been optimized, including one where an electron is transferred 8 A from the disulfide to the substrate simultaneously with a proton transfer from Glu441. The calculated barrier for this step is 19.1 kcal/mol, which can be compared to the rate-limiting barrier indicated by experiments of about 17 kcal/mol. Even though the calculated barrier is somewhat higher than the experimental limit, the discrepancy is within the normal error bounds of B3LYP. The suggestion from the present modeling study is thus that a protonated Glu441 does not need to be present at the active site from the beginning of the catalytic cycle. However, the previously suggested mechanism with an initial protonation of Glu441 cannot be ruled out, because even with the cost added for protonation of Glu441 with a typical pK(a) of 4, the barrier for that mechanism is lower than the one obtained for the present mechanism. The results are compared to experimental results and suggestions.     

Beryllium dimer,a critical test case of MBPT and CI methods

The ground-state potential curve for the beryllium dimer is calculated as a critical test case for methods based on many-body perturbation theory (MBPT ) and configuration interaction (CI ). In particular, the recently proposed double excitation (DE ) MBPT method is compared to the standard SCF-CI method including single and double excitations from a single reference determinant. The SCF-CI method is shown to give surprisingly accurate results compared to more complete CI calculations including a larger configuration space, whereas the DE-MBPT method breaks down more or less completely, particularly for larger basis sets. The results thus demonstrate the importance of including the renormalization terms in this case. Finally, Davidson's correction and related methods lead to an even more severe breakdown than the DE-MBPT method.     

Fluorine core esca linewidths in CH3F and CF4

Ab initio calculations within the Hartree-Fock formation have been carried out on potential energy surfaces of the ground and the F_1s hole states of CH₃F and CF₄ in order to investigate linewidths of their ESCA spectra. The calculations show that potential energy surfaces of both hole states have dissociative character and can be approximated by straight lines in the region of interest. A simple formula for the ESCA fwhm linewidth is derived which yields results in good agreement with experiment. Theoretically derived relaxation and Koopmans' energies have been investigated as a function of geometry.     

Electronic correlation contribution to the three-body potentials for water trimers

A number of trimers of water molecules have been computed with an extended basis set in the Hartree–Fock and in the direct CI approximations. It has been verified that the three-body interaction energy can be calculated within the Hartree–Fock method. Therefore, the correlation corrections to the Hartree–Fock level are essentially additive and do not contribute significantly to three-body effects.     

Theoretical models for the oxygen radical mechanism of water oxidation and of the water oxidizing complex of photosystem II

Hybrid density functional theory is used to study reasonably realistic models of the oxygen-evolving manganese complex in photosystem II. Since there is not yet any X-ray structure of the complex, other types of experimental and theoretical information are used to construct the model complexes. In these complexes, three manganese centers are predicted to be closely coupled by mu-oxo bonds in a triangular orientation. Using these models, the previously suggested oxygen radical mechanism for O2 formation is reinvestigated. It is found that the oxygen radical in the S3 state now appears in a bridging position between two manganese atoms. It is still suggested that only one manganese atom is redox-active. Instead, a number of surprisingly large trans-effects are found, which motivate the existence and define the function of the other manganese atoms in the Mn4 cluster. Calcium has a strong chelating effect which helps in the creation of the necessary oxygen radical. In the present model the chemistry preceding the actual O-O bond formation occurs in an incomplete cube with a missing corner and with two manganese and one calcium in three of the corners. The external water providing the second oxygen of O2 enters in the missing corner of the cube. The present findings are in most cases in good agreement with experimental results as given in particular by EXAFS.     

Modeling aspects of mechanisms for reactions catalyzed by metalloenzymes

Different models to treat metal‐catalyzed enzyme reactions are investigated. The test case chosen is the recently suggested full catalytic cycle of manganese catalase including eight different steps. This cycle contains O? O and O? H activations, as well as electron transfer steps and redox active reactions, and is therefore believed to be representative of many similar systems. Questions concerning modeling of ligands and the accuracy of the computational model are studied. Imidazole modeling of histidines are compared to ammonia modeling, and formate modeling compared to acetate modeling of glutamates. The basis set size required for the geometry optimization and for the final energy evaluation is also investigated. The adequacy of the model is judged in relation to the inherent accuracy achievable with the hybrid DFT method B3LYP. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1634–1645, 2001