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The photochemical decomposition of ethyl(aqua)cobaloxime, [EtCo III (dmgH) 2 H 2 O], a vitamin B 12 derivative model complex, was investigated to understand the mechanism of the Co-C Et bond scission induced by light. Upon irradiation of [EtCo III (dmgH) 2 H 2 O], the Co-C Et bond undergoes homolytic scission, resulting in Et/Co(II) radical pair (RP) formation in a similar fashion observed in alkylcobalamins. The [EtCo III (dmgH) 2 H 2 O] complex acts as a potent quencher of a wide variety of excited states in the presence of organic molecules such as benzophenone. It has been proposed that the reaction mechanism involves Dexter energy transfer, resulting in the bond dissociation process. Two issues associated with the proposed mechanism have been investigated, namely, (i) how the energy transfer occurs from benzophenone to cobaloxime and (ii) how the Co-C Et bond is activated and cleaved. Both TD-DFT and CASSCF/NEVPT2 methods have been applied to show the feasibility of the energy transfer reaction via the triplet pathway from photocatalyst to substrate.

Methyl transfer reactions, mediated by methyltransferases (MeTrs), such as methionine synthase (MetH) or monomethylamine: CoM (MtmBC), constitute one of the most important classes of vitamin B 12 -dependent reactions. The challenge in exploring the catalytic function of MeTrs is related to their modular structure. From the crystallographic point of view, the structure of each subunit has been determined, but there is a lack of understanding of how each subunit interacts with each other. So far, theoretical studies of methyl group transfer were carried out for the structural models of the active site of each subunit. However, those studies do not include the effect of the enzymatic environment, which is crucial for a comprehensive understanding of enzyme-mediated methyl transfer reactions. Herein, to explore how two subunits interact with each other and how the methyl transfer reaction is catalyzed by MeTrs, molecular docking of the functional units of MetH and MtmBC was carried out. Along with the interactions of the functional units, the reaction coordinates, including the Co-C bond distance for methylation of cob(I)alamin (Co I Cbl) and the C-S bond distance in demethylation reaction of cob(III)alamin (Co III Cbl), were considered. The functional groups should be arranged so that there is an appropriate distance to transfer a methyl group and present results indicate that steric interactions can limit the number of potential arrangements. This calls into question the possibility of S N 2-type mechanism previously proposed for MeTrs. Further, it leads to the conclusion that the methyl transfer reaction involves some spatial changes of modules suggesting an alternate radical-based pathway for MeTrs-mediated methyl transfer reactions. The calculations also showed that changes in torsion angles induce a change in reaction coordinates, namely Co-C and C-S bond distances, for the methylation and demethylation reactions catalyzed both by MetH and MtmBC., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Polarized X-ray absorption near-edge structure (XANES) at the Co K-edge and broadband UV-vis transient absorption are used to monitor the sequential evolution of the excited-state structure of coenzyme B 12 (adenosylcobalamin) over the first picosecond following excitation. The initial state is characterized by sub-100 fs sequential changes around the central cobalt. These are polarized first in the y -direction orthogonal to the transition dipole and 50 fs later in the x -direction along the transition dipole. Expansion of the axial bonds follows on a ca. 200 fs time scale as the molecule moves out of the Franck-Condon active region of the potential energy surface. On the same 200 fs time scale there are electronic changes that result in the loss of stimulated emission and the appearance of a strong absorption at 340 nm. These measurements provide a cobalt-centered movie of the excited molecule as it evolves to the local excited-state minimum.

We use picosecond time-resolved polarized X-ray absorption near-edge structure (XANES) measurements to probe the structure of the long-lived photoexcited state of methylcobalamin (MeCbl) and the cob(II)alamin photoproduct formed following photoexcitation of adenosylcobalamin (AdoCbl, coenzyme B 12 ). For MeCbl, we used 520 nm excitation and a time delay of 100 ps to avoid the formation of cob(II)alamin. We find only small spectral changes in the equatorial and axial directions, which we interpret as arising from small (<∼0.05 Å) changes in both the equatorial and axial distances. This confirms expectations based on prior UV-visible transient absorption measurements and theoretical simulations. We do not find evidence for the significant elongation of the Co-C bond reported by Subramanian [ J. Phys. Chem. Lett. 2018 , 9 , 1542 - 1546 ] following 400 nm excitation. For AdoCbl, we resolve the difference XANES contributions along three unique molecular axes by exciting with both 540 and 365 nm light, demonstrating that the spectral changes are predominantly polarized along the axial direction, consistent with the loss of axial ligation. These data suggest that the microsecond "recombination product" identified by Subramanian et al. is actually the cob(II)alamin photoproduct that is produced following bond homolysis of MeCbl with 400 nm excitation. Our results highlight the pronounced advantage of using polarization-selective transient X-ray absorption for isolating structural dynamics in systems undergoing atomic displacements that are strongly correlated to the exciting optical polarization.

Glutamate mutase (GLM) is a coenzyme B 12 -dependent enzyme that catalyzes the conversion of S-glutamate to (2 S,3 S)-3-methyl aspartate. The initial step in the catalytic process is the homolytic cleavage of the coenzyme's Co-C bond upon binding of a substrate. Alternatively, the Co-C bond can be cleaved using light. To investigate the photolytic cleavage of the Co-C bond in GLM, we applied a combined density functional theory/molecular mechanics (DFT/MM) and time-dependent-DFT/MM method to scrutinize the ground and the low-lying excited states. Potential energy surfaces (PESs) were generated as a function of axial bond lengths to describe the photodissociation mechanism. The S 1 PES was characterized as the crossing of two electronic states, metal-to-ligand charge transfer (MLCT), and ligand field (LF). In GLM, radical pairs generate from the LF state. Two pathways, path A and path B, were identified as possible channels to connect the MLCT and LF electronic states. The S 1 PES in GLM was compared with the S 1 PES for coenzyme B 12 -dependent ethanolamine ammonia lyase as well as the isolated AdoCbl cofactor. Finally, the theoretical insights related to the photodissociation mechanism were compared with transient absorption spectroscopy, electron paramagnetic resonance, and resonance Raman spectroscopy.

Vitamin B 12 -dependent enzymes catalyze several difficult radical reactions. There are fundamental open questions that need to be addressed to fully understand the formation of highly reactive radical species, its dynamics, and interaction with the substrate and enzyme. In this work, ab initio molecular dynamics was performed within a QM/MM framework on a reduced AdoCbl cofactor, which was taken as a post proton-coupled electron transfer initial step for the activation of the AdoCbl-dependent methylmalonyl CoA mutase enzyme. The calculated free-energy profile reveals two possible pathways, stepwise (I) and concerted (II) for the reductive Co-C cleavage and subsequent H-abstraction. The computed activation barrier from metadynamics for both the pathways is comparable (78.5 and 76.2 kJ/mol, respectively); however, the concerted pathway may be preferred kinetically because it avoids the formation of a high-energy radical intermediate with possibly a larger recrossing rate. Our results are consistent with the previous conductor hypothesis, indicating the explicit role of cob(II)alamin in stabilizing the radical intermediate involved in the H-atom transfer.

Ultrafast time-resolved spectroscopy was used to study the photochemistry of hydroxocobalamin (HOCbl) and aquocobalamin (H 2 OCbl + ) in solution. Spectroscopic measurements and TD-DFT simulations provide a consistent picture of the spectroscopy and photochemistry. Excitation of H 2 OCbl + results in formation of an excited state followed by rapid internal conversion to the ground state (0.35 ± 0.15 ps) through an S 1 /S 0 seam at a slightly elongated Co-O bond length and a significantly elongated Co-N Im bond length. In contrast, the initial elongation of the axial bonds in HOCbl is followed by contraction to an excited state minimum with bonds slightly shorter than those in the ground state. Internal conversion to the ground state follows on a picosecond time scale (5.3 ± 0.4 ps). For both compounds, photodissociation forming cob(II)alamin and hydroxyl radicals (∼1.5% yield) requires excitation to highly excited states. Dissociation is mediated by competition between internal conversion to the S 1 surface and prompt bond cleavage.

Polarized ultrafast time-resolved X-ray absorption near edge structure (XANES) allows characterization of excited state dynamics following excitation. Excitation of vitamin B 12 , cyanocobalamin (CNCbl), in the αβ-band at 550 nm and the γ-band at 365 nm was used to uniquely resolve axial and equatorial contributions to the excited state dynamics. The structural evolution of the excited molecule is best described by a coherent ballistic trajectory on the excited state potential energy surface. Prompt expansion of the Co cavity by ca. 0.03 Å is followed by significant elongation of the axial bonds (>0.25 Å) over the first 190 fs. Subsequent contraction of the Co cavity in both axial and equatorial directions results in the relaxed S 1 excited state structure within 500 fs of excitation.

In a comment on our article "Theory of Thomson scattering in inhomogeneous media", V. V. Belyi asserts that there is an inconsistency in our method of applying gradient effects via the dielectric superposition principle, in violation of the fluctuation-dissipation theorem; and that his Klimontovich-Langevin formulation would be more appropriate to our application. While we agree that a generalization, along the lines of Belyi's work, would be required for strongly coupled systems, for the weakly coupled systems which we considered, these corrections are not necessary and our approach is still appropriate.Replying to: V. Belyi, Sci. Rep. 8 (2018); https://doi.org/10.1038/s41598-018-25319-6 .

Thomson scattering of laser light is one of the most fundamental diagnostics of plasma density, temperature and magnetic fields. It relies on the assumption that the properties in the probed volume are homogeneous and constant during the probing time. On the other hand, laboratory plasmas are seldom uniform and homogeneous on the temporal and spatial dimensions over which data is collected. This is particularly true for laser-produced high-energy-density matter, which often exhibits steep gradients in temperature, density and pressure, on a scale determined by the laser focus. Here, we discuss the modification of the cross section for Thomson scattering in fully-ionized media exhibiting steep spatial inhomogeneities and/or fast temporal fluctuations. We show that the predicted Thomson scattering spectra are greatly altered compared to the uniform case, and may lead to violations of detailed balance. Therefore, careful interpretation of the spectra is necessary for spatially or temporally inhomogeneous systems.

Density functional theory (DFT) has been applied to investigate the structural and electronic properties of an [(Al2O3)4](+) cluster. Since there is no structural data available from experiment, the geometry of the cluster was obtained based on a model which produced the best agreement with vibrational IR-MPD data. A range of different exchange-correlation functionals were tested, and it was concluded that the best spectral agreement was produced using the CAM-B3LYP and B3LYP functionals, respectively. To further characterize the properties of the cluster, natural bond order analysis was performed, and it was concluded that an appropriate description for the system is [Al8O12](+). The frontier orbitals and spin densities of both cation and neutral systems were considered, and it was concluded that the unrestricted singlet and triplet spin densities of the neutral [Al8O12] system were nearly degenerate, representing a di-radical, with the triplet state being lower in energy.

A mechanism of Co-C bond photolysis in the base-off form of the methylcobalamin cofactor (MeCbl) and the influence of its axial base on Co-C bond photodissociation has been investigated by time-dependent density functional theory (TD-DFT). At low pH, the MeCbl cofactor adopts the base-off form in which the axial nitrogenous ligand is replaced by a water molecule. Ultrafast excited-state dynamics and photolysis studies have revealed that a new channel for rapid nonradiative decay in base-off MeCbl is opened, which competes with bond dissociation. To explain these experimental findings, the corresponding potential energy surface of the S1 state was constructed as a function of Co-C and Co-O bond distances, and the manifold of low-lying triplets was plotted as a function of Co-C bond length. In contrast to the base-on form of MeCbl in which two possible photodissociation pathways were identified on the basis of whether the Co-C bond (path A) or axial Co-N bond (path B) elongates first, only path B is active in base-off MeCbl. Specifically, path A is inactive because the energy barrier associated with direct dissociation of the methyl ligand is higher than the barrier of intersection between two different electronic states: a metal-to-ligand charge transfer state (MLCT), and a ligand field state (LF) along the Co-O coordinate of the S1 PES. Path B initially involves displacement of the water molecule, followed by the formation of an LF-type intermediate, which possesses a very shallow energy minimum with respect to the Co-C coordinate. This LF-type intermediate on path B may result in either S1/S0 internal conversion or singlet radical pair generation. In addition, intersystem crossing (ISC) resulting in generation of a triplet radical pair is also feasible.

A mechanism of Co-C bond photodissociation in the base-on form of the methylcobalamin cofactor (MeCbl) has been investigated employing time-dependent density functional theory (TD-DFT), in which the key step involves singlet radical pair generation from the first electronically excited state (S1). The corresponding potential energy surface of the S1 state was constructed as a function of Co-C and Co-Naxial bond distances, and two possible photodissociation pathways were identified on the basis of energetic grounds. These pathways are distinguished by whether the Co-C bond (path A) or Co-Naxial bond (path B) elongates first. Although the final intermediate of both pathways is the same (namely a ligand field (LF) state responsible for Co-C dissociation), the reaction coordinates associated with paths A and B are different. The photolysis of MeCbl is wavelength-dependent, and present TD-DFT analysis indicates that excitation in the visible α/β band (520 nm) can be associated with path A, whereas excitation in the near-UV region (400 nm) is associated with path B. The possibility of intersystem crossing, and internal conversion to the ground state along path B are also discussed. The mechanism proposed in this study reconciles existing experimental data with previous theoretical calculations addressing the possible involvement of a repulsive triplet state.

Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive (3)(σCo-C → σ(*) Co-C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a metal-to-ligand charge transfer (MLCT) and a σ bonding-ligand charge transfer (SBLCT) states.

Methionine synthase (MetH) catalyzes the transfer of a methyl group from methyltetrahydrofolate (CH3-H4Folate) to the cob(I)alamin intermediate to form an organometallic Co-C bond, a reaction similar to that of CH3-H4Folate:corrinoid/iron-sulfur protein (CFeSP) methyltransferase (MeTr). How precisely it is formed remains elusive because the displacement of a methyl group from the tertiary amine is not a facile reaction. To understand the electronic structure and mechanistic details of the MetH-cob(I)alamin:CH3-H4Folate reaction complex, we applied quantum mechanics/molecular mechanics (QM/MM) computations. The hybrid QM/MM calculations reveal the traditionally assumed SN2 mechanism for formation the CH3-cob(III)alamin resting state where the activation energy barrier for the SN2 reaction was found to be ~8-9 kcal/mol, which is comparable with respect to the determined experimental rate constant. However, the possibility of an electron transfer (ET) based radical mechanism consistent with the close-lying diradical states observed from triplet and open-shell singlet states has also been suggested as an alternative, where first an electron transfer from His-on cob(I)alamin to the pterin ring of the protonated CH3-H4Folate takes place, forming the Co(II)(d(7))-pterin radical (π*)(1) diradical state, followed by a methyl radical transfer. Although the predicted energy barrier for the ET-mediated radical reaction is comparable to that of the SN2 pathway, the major advantage of ET is that a methyl radical can be transferred at a longer distance, which does not require the close proximity of two binding modules of MetH as does the SN2 type. In addition, based on the energy barrier of the transition state (TS) in both the protonated (~8-9 kcal/mol) and the unprotonated N5 (39 kcal/mol) species of the CH3-H4Folate, it can be inferred that the protonation event must takes place either prior to or during the methyl transfer reaction in a ternary complex. The results of the present study including mechanistic insights can have implications to a broad class of corrinoid-methyltransferases, which utilize a CH3-H4Folate substrate or its related analogues as methyl donor.

The nature of electronically excited states of the super-reduced form of vitamin B(12) (i.e., cob(I)alamin or B(12s)), a ubiquitous B(12) intermediate, was investigated by performing quantum-chemical calculations within the time-dependent density functional theory (TD-DFT) framework and by establishing their correspondence to experimental data. Using response theory, the electronic absorption (Abs), circular dichroism (CD) and magnetic CD (MCD) spectra of cob(I)alamin were simulated and directly compared with experiment. Several issues have been taken into considerations while performing the TD-DFT calculations, such as strong dependence on the applied exchange-correlation (XC) functional or structural simplification imposed on the cob(I)alamin. In addition, the low-lying transitions were also validated by performing CASSCF/MC-XQDPT2 calculations. By comparing computational results with existing experimental data a new level of understanding of electronic excitations has been established at the molecular level. The present study extends and confirms conclusions reached for other cobalamins. In particular, the better performance of the BP86 functional, rather than hybrid-type, was observed in terms of the excitations associated with both Co d and corrin π localized transitions. In addition, the lowest energy band was associated with multiple metal-to-ligand charge transfer excitations as opposed to the commonly assumed view of a single π → π* transition followed by vibrational progression. Finally, the use of the full cob(I)alamin structure, instead of simplified molecular models, shed new light on the spectral analyses of cobalamin systems and revealed new challenges of this approach related to long-range charge transfer excitations involving side chains.

The imidazole side-chains of histidine residues perform key roles in proteins, and spectroscopic markers are of great interest. The imidazole Raman spectrum is subject to resonance enhancement at UV wavelengths, and a number of UVRR markers of structure have been investigated. We report a systematic experimental and computational study of imidazole UVRR spectra, which elucidates the band pattern, and the effects of protonation and deprotonation, of H/D exchange, of metal complexation, and of addition of a methyl substituent, modeling histidine itself. A consistent assignment scheme is proposed, which permits tracking of the bands through these chemical variations. The intensities are dominated by normal mode contributions from stretching of the strongest ring bonds, C(2)N and C(4)C(5), consistent with enhancement via resonance with a dominant imidazole π-π* transition.

Time-dependent density functional theory (TD-DFT) has been applied to explore electronically excited states of vitamin B(12) (cyanocobalamin or CNCbl). To explain why the Co-C bond in CNCbl does not undergo photodissociation under conditions of simple photon excitation, electronically excited states have been computed along the Co-C(CN) stretched coordinate. It was found that the repulsive (3)(σ(Co-C) → σ*(Co-C)) triplet state drops in energy as the Co-C(CN) bond lengthens, but it does not become dissociative. Low-lying excited states were also computed as function of two axial bond lengths. Two energy minima have been located on the S(1)/CNCbl, as well as T(1)/CNCbl, surfaces. The full geometry optimization was carried out for each minimum and electronic properties associated with each optimized structure were analyzed in details. One minimum was described as excitation having mixed ππ*/MLCT (metal-to-ligand charge transfer) character, while the second as ligand-to-metal charge transfer (LMCT) transition. Neither of them, however, can be viewed as pure MLCT or LMCT transitions since additional excitation to or from σ-bonds (SB) of N-Co-C unit have also noticeable contributions. Inclusion of solvent altered the character of one of the excitations from ππ*/MLCT/SBLCT to ππ*/LMCT/LSBCT-type, and therefore, both of them gained significant contribution from LMCT/LSBCT transition. Finally, the nature of S(1) electronic state has been comparatively analyzed in CNCbl and MeCbl cobalamins.

Complete active space self-consistent field (CASSCF) computations followed by the second-order perturbation theory have been applied to investigate the electronic properties of a structural mimic of the reactant complex formed in the catalytic cycle of cobalamin-dependent methionine synthase (MetH). Two different structural models have been employed to analyze the reaction complex between methylcobalamin (MeCbl) and homocysteine (Hcy). The first model, referred to as the small model (SM), is based on a truncated corrin ring with inner conjugated macrocycle only and has symmetry constrain with respect to methylthiolate. The second is based on a full corrin ring, i.e., [Co(III)(corrin)]-Me(+)···(-)S-CH(3), without the side chains (which were replaced by hydrogen atoms) and referred to as the large model (LM). The active space chosen for both models includes all essential orbitals participating in the methyl transfer reaction. Although the CASSCF calculations are much more demanding for the LM (due to the structural complexity) than the SM, the results are fully consistent. The energetic of ionic and diradical states have been examined as a function of the C···S distance between the methyl group of MeCbl and the sulfur of the thiolate substrate for both models. The most important finding of the present work is the energetic variation of ionic and diradical states as a function of C···S distance. The two states cross each other at a C···S distance of 4.0 Å, i.e., for a distance shorter than ∼4.0 Å, the ionic state is energetically the lowest electronic state, while the diradical state becomes the lowest state at longer distances. However, the potential energy surface of the ionic state shows greater sensitivity with respect to the C···S distance than that of the diradical one. The former can be associated with S(N)2-type displacement, where the cleavage of the Co-C bond would be heterolytic, while the latter can be associated with an electron transfer (ET), where the cleavage is homolytic. Finally, the importance of this finding is briefly discussed in the context of MeCbl-dependent enzymatic catalysis.

Time-dependent density functional theory (TD-DFT) and correlated ab initio methods have been applied to explore the electronically excited states of vitamin B(12) (cyanocobalamin or CNCbl). Different experimental techniques have been used to probe the excited states of CNCbl, revealing many issues that remain poorly understood from an electronic structure point of view. Due to its efficient scaling with size, TD-DFT emerges as one of the most practical tools that can be used to study the electronic properties of these fairly complex molecules. However, the description of excited states is strongly dependent on the type of functional used in the calculations. In the present contribution, the choice of a proper functional for vitamin B(12) was evaluated in terms of its agreement with both experimental results and correlated ab initio calculations. Three different functionals, i.e., B3LYP, BP86, and LC-BLYP, were tested. In addition, the effect of the relative contributions of DFT and HF to the exchange-correlation functional was investigated as a function of the range-separation parameter, μ. The issues related to the underestimation of charge-transfer excitation energies by TD-DFT were validated by the Λ diagnostic, which measures the spatial overlap between occupied and virtual orbitals involved in the particular excitation. The nature of the low-lying excited states was also analyzed based on a comparison of TD-DFT and ab initio results. Based on an extensive comparison with experimental results and ab initio benchmark calculations, the BP86 functional was found to be the most appropriate in describing the electronic properties of CNCbl. Finally, an analysis of electronic transitions and reassignment of some excitations were discussed.

Linear and quadratic response time-dependent density functional theory (TD-DFT) has been applied to investigate absorption (Abs), circular dichroism (CD), and magnetic CD (MCD) spectra of cyanocobalamin (CNCbl) and methylcobalamin (MeCbl). Although electronically excited states of both cobalamins have been probed by applying different experimental techniques, their exact nature remains poorly understood from an electronic structure point of view. Recent theoretical studies have revealed a lot of relevant information about their properties but also left some unresolved issues related to the nature of individual transitions. In this contribution, not only Abs but also CD and MCD spectra of both cobalamins were computed for direct comparison with experiment. The results were evaluated with respect to the choice of exchange-correlation functional, basis set, and the environment (gas phase or solvent) used in the calculation. Taking into account the complexity of the CNCbl and MeCbl systems, reliable agreement between theory and experiment was achieved based on calculations employing the BP86 functional, particularly for the low-energy α/β bands. This spectral range has been traditionally interpreted as a vibrational progression associated with a single electronic excitation, but according to the present analysis for both cobalamins, these bands are best interpreted as consisting of multiple electronic transitions.

The key step in the catalytic cycle of methionine synthase (MetH) is the transfer of a methyl group from the methylcobalamin (MeCbl) cofactor to homocysteine (Hcy). This mechanism has been traditionally viewed as an S(N)2-type reaction, but a different mechanism based on one-electron reduction of the cofactor (reductive cleavage) has been recently proposed. In this work, we analyze whether this mechanism is plausible from a theoretical point of view. By means of a combination of gas-phase as well as hybrid QM/MM calculations, we show that cleavage of the Co-C bond in a MeCbl···Hcy complex (Hcy = methylthiolate substrate (Me-S(-)), a structural mimic of deprotonated homocysteine) proceeds via a [Co(III)(corrin(*-))]-Me···*S-Me diradical configuration, involving electron transfer (ET) from a π*(corrin)-type state to a σ*(Co-C) one, and the methyl transfer displays an energy barrier ≤8.5 kcal/mol. This value is comparable to the one previously computed for the alternative S(N)2 reaction pathway (10.5 kcal/mol). However, the ET-based reductive cleavage pathway does not impose specific geometrical and distance constraints with respect to substrate and cofactor, as does the S(N)2 pathway. This might be advantageous from the enzymatic point of view because in that case, a methyl group can be transferred efficiently at longer distances.

Detailed theoretical and X-ray based structural analysis has been carried out in order to unmask the role of the tyrosine residue (Y) in the activation of the Co-C bond in AdoCbl-dependent mutases. In particular, methylmalonyl-CoA mutase (MCM) and glutamate mutase (GLM) enzymes have been studied; in the case of MCM, the significance of the Y89 residue has been analyzed extensively. Three different theoretical platforms encompassing the DFT, CASSCF/QDPT2, and QM/MM frameworks have been employed to elucidate the energetics of the AdoCbl-Y(-) complex while taking into account a varied degree of structural complexity. The diradical state, [AdoCbl](*-)-Y*, has been found to be the lowest electronic state of the AdoCbl-Y(-) complex, providing strong evidence that electron transfer from the Y89 residue to the cofactor is feasible. Crystallographic analysis of the active sites of MCM and GLM enzymes reveals that substrate binding can play a critical role in displacing the hydroxyl proton of the Y residue (Y89 in the case of MCM enzyme and Y181 in the case of GLM enzyme) that will facilitate the electron transfer (ET), hence making the activation process a case of proton-coupled electron transfer (PCET). PCET-inspired enzymatic catalysis implies that the cleavage of the Co-C bond takes place via one-electron reduced form of the AdoCbl cofactor (i.e., [AdoCbl](*-)), rather than its neutral analogue, thus providing an efficient mode of cleavage that can help in understanding the origin of the catalytic effect in such enzymes.

Density functional theory has been applied to study the origin of the inverse and normal trans influence in alkylcobalamins. In order to cover the X-ray structural data available for alkylcobalamins with a variety of axial substituents, geometries of 28 related corrin-containing models have been optimized and analyzed. The BP86/6-31G(d) level of theory was applied which showed good reliability in reproducing the axial bond lengths. Comparison of experimental and calculated data allowed to conclude that the inverse trans influence is not a general feature of cobalamins, as it appeared from the experimental data analysis alone. Inverse trans influence is observed for the series of R groups with increasing bulk and electron donating ability. For the series of R groups having similar medium bulk, but differing significantly in the electron donating ability, normal trans influence was found. Finally, it was determined, that the axial bond lengths correlate well but differently in the two series of R groups with the orbital energies of the six molecular orbitals essential in axial interligand bonding.

The mechanism of Co-C bond photodissociation in methylcobalamin (MeCbl) and ethylcobalamin (EtCbl) has been examined by means of time-dependent density functional theory (TD-DFT). The present contribution extends our recent study (J. Phys. Chem. B 2007, 111, 2419-2422) where relevant excited states involved in the photolysis of MeCbl have been identified. To obtain reliable structural models, the high-resolution crystal structure of MeCbl was used as the source of initial coordinates. The full MeCbl was simplified by replacing the corrin side chains by H atoms and the resulting geometry was optimized. The model of EtCbl was generated from the simplified structure of MeCbl by replacing methyl group with ethyl. For both models, the low-lying singlet and triplet excited states have been computed along the Co-C coordinate at TD-DFT/BP86/6-31G(d) level of theory. These calculations reveal that the photodissociation process is mediated by the repulsive 3(sigmaCo-C-->sigma*Co-C) triplet state. The overall mechanism of photodissociation for both systems is similar but energetic details are different, reflecting the difference in Co-C bond strength in MeCbl and EtCbl. In both cases the key intermediate involved in Co-C bond photodissociation is identified as first excited state (S1). The S1 intermediate has mixed character: it can be described as predominantly dCo-->pi*corrin metal-to-ligand charge transfer (MLCT) state with contribution from sigma bond to corrin charge transfer (SBLCT) where upon electronic excitation the electron density shifts from the axial NIm-Co-C bonding to corrin ligand. The optimized geometry of the S1 indicates that the structure of the corrin remains essentially unchanged in comparison to ground state (S0). The major structural change occurs in the NIm-Co-C moiety, which becomes bent with elongated Co-C bond in S1 state. Finally, it is proposed that the photolysis of Co-C bond is in line with the mechanism of heme-CO photolysis, where participation of the dFe-->pi*porphyrin has been suggested.

Density functional theory has been applied to a series of unsubstituted planar metalloporphyrins (MPs) to elucidate how geometry and frequencies correlate with the metal-nitrogen distance, referred to as the core size. Different transition metals can invoke expansion or contraction of the porphyrin core due to electronic effects resulting from the amount of d-electron pairing as well as occupancy of the d(x(2)(-y(2))) orbital. A full vibrational analysis consisting of all in-plane and out-of-plane frequencies was carried out, and the resulting modes were plotted against core size for a linear analysis and grouped within symmetry blocks. The modes were separated according to planarity, and all modes with a large slope and best fit greater than 0.8 were considered sensitive to metal-nitrogen distances. All planar skeletal modes above 1450 cm(-1), including the pyrolle ring deformations, are found to be core-size sensitive. The most significant out-of-plane modes sensitive to core size are gamma(8) and gamma(9), which are infrared active and grouped within the A(2u) symmetry block. The present work also opens possible quantitative applications for the correlation of spectroscopic properties of MPs and heme proteins with actual structural parameters.

Density functional theory (DFT) has been applied to the analysis of the structural and electronic properties of the alkyl-cobalt(III) phthalocyanine complexes, [CoIIIPc]-R (Pc = phthalocyanine, R = Me or Et), and their pyridine adducts. The BP86/6-31G(d) level of theory shows good reliability for the optimized axial bond lengths and bond dissociation energies (BDEs). The mechanism of the reductive cleavage was probed for the [CoIIIPc]-Me complex which is known as a highly effective methyl group donor. In the present analysis, which follows a recent study on the reductive Co-C bond cleavage in methylcobalamin (J. Phys. Chem. B 2007, 111, 7638-7645), it is demonstrated that addition of an electron and formation of the pi-anion radical [CoIII(Pc*)]-Me- significantly lowers the energetic barrier required for homolytic Co-C bond dissociation. Such BDE lowering in [CoIII(Pc*)]-Me- arises from the involvement of two electronic states: upon electron addition, a quasi-degenerate pi*Pc state is initially formed, but when the cobalt-carbon bond is stretched, the unpaired electron moves to a sigma*Co-C state and the final cleavage involves the three-electron (sigma)2(sigma*)1 bond. As in corrin complexes, the pi*Pc-sigma*Co-C states crossing does not take place at the equilibrium geometry of [CoIII(Pc*)]-Me- but only when the Co-C bond is stretched to approximately 2.3 A. The DFT computed Co-C BDE of 23.3 kcal/mol in the one-electron-reduced phthalocyanine species, [CoIII(Pc*)]-Me-, is lowered by approximately 37% compared to the neutral Py-[CoIIIPc]-Me complex where BDE = 36.8 kcal/mol. A similar comparison for the corrin-containing complexes shows that a DFT computed BDE of 20.4 kcal/mol for [CoIII(corrin*)]-Me leads to approximately 45% bond strength reduction, in comparison to 37.0 kcal/mol for Im-[CoIII(corrin)]-Me+. These results suggest some preference by the alkylcorrinoids for the reductive cleavage mechanism.

Density functional theory has been applied to the investigation of the reductive cleavage mechanism of methylcobalamin (MeCbl). In the reductive cleavage of MeCbl, the Co-C bond is cleaved homolytically, and formation of the anion radical ([MeCbl]*-) reduces the dissociation energy by approximately 50%. Such dissociation energy lowering in [MeCbl]*- arises from the involvement of two electronic states: the initial state, which is formed upon electron addition, has dominant pi*corrin character, but when the Co-C bond is stretched the unpaired electron moves to the sigma*Co-C state, and the final cleavage involves the three-electron (sigma)2(sigma*)1 bond. The pi*corrin-sigma*Co-C states crossing does not take place at the equilibrium geometry of [MeCbl]*- but only when the Co-C bond is stretched to 2.3 A. In contrast to the neutral cofactor, the most energetically efficient cleavage of the Co-C bond is from the base-off form. The analysis of thermodynamic and kinetic data provides a rationale as to why Co-C cleavage in reduced form requires prior departure of the axial base. Finally, the possible connection of present work to B12 enzymatic catalysis and the involvement of anion-radical-like [MeCbl]*- species in relevant methyl transfer reactions is discussed.

In this work we analyze the structure of coenzyme B12 (AdoCbl) by means of periodic density functional theory (DFT) in order to elucidate the influence of the corrin side chains and the crystalline environment on the properties of axial bonds. The Co-Nax axial bond is very weak and its strength of less than 8 kcal/mol is four times smaller than Co-C which in solution is approximately 31 kcal/mol. The proper description of the Co-Nax distance has been problematic in previous DFT calculations and the source of disagreement between experiment and theory remained unexplained. To resolve this discrepancy, periodic DFT calculations within the Car-Parrinello molecular dynamics (CPMD) framework were carried out on three different structural models of increased complexity. The simplest model (DBI-Ado+) contains the naked corrin ring with a total of 96 atoms. The second model is the full coenzyme B12 (AdoCbl) with 209 atoms which has been taken from crystallographic analysis. To understand the extent to which the crystal packing forces influence the structural properties of AdoCbl the complete crystal consisting of four AdoCbl molecules plus 48 water molecules periodically repeated in space was analyzed (1008 atoms). The results show that the properties associated with the Co-C bond can be well reproduced using truncated models. This does not apply to the Co-Nax axial bond and the presence of the local environment appears to be essential for the correct prediction of its bond length. The most interesting outcome of the present analysis is the finding that the actual length of the Co-Nax bond (2.262 A) is largely influenced by crystal packing forces.

The relevant excited states involved in the photolysis of methylcobalamin (MeCbl) have been examined by means of time-dependent density functional theory (TD-DFT). The low-lying singlet and triplet excited states have been calculated along the Co-C bond at the TD-DFT/BP86/6-31g(d) level of theory in order to investigate the dissociation process of MeCbl. These calculations have shown that the photodissociation is mediated by the repulsive 3(sigmaCo-C --> sigma*Co-C) triplet state. The key metastable photoproduct involved in Co-C bond photolysis was identified as an S1 state having predominantly dCo --> pi*corrin metal-ligand charge transfer (MLCT) character.

The vibronic (vibrational-electronic) interactions in the pi-anion radicals of the metalloporphyrins (M=Cr, Mn, Fe, Co, Ni, Cu, and Zn), which show delocalized D4h structures in the neutral states, are discussed using B3LYP density-functional-theory calculations. The B1g and B2g modes of vibration can remove the degenerate 2Eg state of the pi-anion radicals in the D4h symmetric structures to lead to rectangular and diamond D2h distortions, respectively. Calculated vibronic coupling constants demonstrate that the B1g modes of vibration better couple with the degenerate electronic state, leading to the rectangular D2h distortion. In particular, the B1g modes of nu10 and nu11, which have dominant contributions from Calpha-Cm and Cbeta-Cbeta stretching, give large vibronic coupling constants in the pi-anion radicals. The vibronic coupling constant can be viewed as the Jahn-Teller distortion force, and therefore these C-C stretching B1g modes will play a central role in the Jahn-Teller effect of the pi-anion radicals of the metalloporphyrins.

Robotic-assisted laparoscopic radical prostatectomy (RLRP) has become an accepted treatment option for men with prostate cancer. A search of the available literature through January 2006 was performed to analyze the surgical technique, outcomes data, and other unique issues regarding RLRP. While prospective, randomized trials and long-term data are lacking, short-term data from single institution series have demonstrated outcomes for RLRP that appear to be equivalent to those for open radical prostatectomy (ORP). Although not yet proven, some encouraging data suggest that RLRP may be able to achieve improved cancer control, postoperative urinary control, and erectile function compared to open surgery for prostate cancer. Definite advantages of RLRP over ORP are not yet established. Future studies will determine the role of RLRP in the surgical treatment of men with prostate cancer.

A method for analyzing the A(1u)/A(2u) contents of metalloporphyrin pi-cation radicals is developed and applied to a series of unsubstituted planar metalloporphines (MPs) (M=Cr, Mn, Fe, Co, Ni, Cu, and Zn). The structures and electronic properties of the MPs and their cation radicals were calculated by density functional theory (DFT) and subsequently analyzed. It was found that the MPs with small core sizes have a tendency to form A(1u)-type radicals, while the MPs with large core size have a preference for an A(2u)-type. Neither of these pure-state species, however, is stable under the D(4)(h) symmetry, and both radical cation types are subject to pseudo-Jahn-Teller (pJT) distortion. The pJT distortion leads to structures with lower symmetry and states that have mixed character with respect to the A(1u) and A(2u) components. The degree of mixing could be estimated by employing orbital projection technique or a complementary spin density decomposition. Both techniques produce very similar results, pointing out that the frontier orbital, which becomes empty upon electron removal, plays a critical role in determining electronic properties.

Inelastic neutron scattering (INS) spectra of free base (FBP) and zinc (ZnP) porphines are presented and compared with the results of density functional theory (DFT) calculations using the B3LYP functional with 6-31G(d) or 6-311G(d,p) basis sets. To obtain quantitative agreement between experiment and theory, two different scaling techniques have been applied: a scaled quantum mechanical (DFT-SQM) force field was developed for B3LYP/6-31G(d) calculations and the uniform frequency scaling technique (DFT-UFS) was applied to B3LYP/6-311G(d,p) results. The DFT-SQM calculations have been previously compared with IR and Raman spectra with good agreement, which allows for a nearly complete vibrational assignment. The results of the present study extend previous vibrational analysis to a higher level of reliability and complexity. The previous results are augmented by the comparison of calculated and observed INS intensities and the comparison of calculated modes with those observed in INS spectra but previously unobserved in optical spectra. Excellent agreement is acquired between the INS spectra and the results of both calculations, permitting a more detailed and reliable description of the vibrational properties of porphyrins.