Apparent or real water exchange reactions on [Zn(H2O)4(L)](2+)·2H2O (L = sp-nitrogen donor ligands)? A quantum chemical investigation

The exchange of a second coordination sphere water molecule in [Zn(H(2)O)(4)(L)](2+)·2H(2)O (L = HN(3), HCN, FCN, ClCN, BrCN, CH(3)CN, (C(4)H(3))CN, PhCN, (CH(3))(3)CCN, CF(3)CN, CCl(3)CN, CHCl(2)CN, and CH(2)ClCN) against a coordinated water molecule was studied by quantum chemical calculations (RB3LYP/6-311+G**). The complete reaction consists of an associative binding of one H(2)O from the second coordination sphere leading to a six-coordinate intermediate [Zn(H(2)O)(5)(L)](2+)·H(2)O, followed by the dissociation of a water molecule to reach the product state [Zn(H(2)O)(4)(L)](2+)·2H(2)O. For a real water exchange reaction to occur two different transition states have to be included, otherwise only an apparent water exchange reaction takes place. For the water exchange reaction in [Zn(H(2)O)(4)(L)](2+)·2H(2)O, nearly iso-energetic cis- and trans-orientated transition states are crossed. The gas-phase proton affinity of L shows instructive correlations with structural parameters and energy gaps for the investigated reactions.     

Water-assisted reaction mechanism of monozinc beta-lactamases

Hybrid Car-Parrinello QM/MM calculations are used to investigate the reaction mechanism of hydrolysis of a common beta-lactam substrate (cefotaxime) by the monozinc beta-lactamase from Bacillus cereus (BcII). The calculations suggest a fundamental role for an active site water in the catalytic mechanism. This water molecule binds the zinc ion in the first step of the reaction, expanding the zinc coordination number and providing a proton donor adequately oriented for the second step. The free energy barriers of the two reaction steps are similar and consistent with the available experimental data. The conserved hydrogen bond network in the active site, defined by Asp120, Cys221, and His263, not only contributes to orient the nucleophile (as already proposed), but it also guides the second catalytic water molecule to the zinc ion after the substrate is bound. The hydrolysis reaction in water has a relatively high free energy barrier, which is consistent with the stability of cefotaxime in water solution. The modeled Michaelis complexes for other substrates are also characterized by the presence of an ordered water molecule in the same position, suggesting that this mechanism might be general for the hydrolysis of different beta-lactam substrates.     

Energetics and mechanisms of C-H bond activation by a doubly charged metal ion: guided ion beam and theoretical studies of Ta2+ + CH4

A guided ion beam tandem mass spectrometer is used to study the kinetic-energy dependence of doubly charged atomic tantalum cations (Ta(2+)) reacting with CH4 and CD4. As for the analogous singly charged system, the dehydrogenation reaction to form TaCH2(2+) + H2 is exothermic. The charge-transfer reaction to form Ta(+) + CH4(+) and the charge-separation reaction to form TaH(+) + CH3(+) are also observed at low energies in exothermic processes, as is a secondary reaction of TaCH2(2+) to form TaCH3(+) + CH3(+). At higher energies, other doubly charged products, TaC(2+) and TaCH3(2+), are observed, although no formation of TaH(2+) was observed. Modeling of the endothermic cross sections provides 0 K bond dissociation energies (in electronvolts) of D0(Ta(2+)-C) = 5.42 +/- 0.19 and D0(Ta(2+)-CH3) = 3.40 +/- 0.16. These experimental bond energies are in poor agreement with density functional calculations at the B3LYP/HW+/6-311++G(3df,3p) level of theory. However, the Ta(2+)-C bond energy is in good agreement with calculations at the QCISD(T) level of theory, and the Ta(2+)-CH3 bond energy is in good agreement with density functional calculations at the BHLYP level of theory. Theoretical calculations reveal the geometric and electronic structures of all product ions and are used to map the potential energy surface, which describes the mechanism of the reaction and key intermediates. Both experimental and theoretical results suggest that TaH(+), TaCH2(2+), and TaCH3(2+) are formed through a H-Ta(2+)-CH3 intermediate.     

Platinum fluorides beyond PtF6?

Quantum-chemical calculations at DFT B3LYP and ab initio MP2, CCSD, and CCSD(T) levels have been performed on various binary fluorides of platinum up to formal oxidation state +VIII, to evaluate the stability of these species. The calculations indicate clearly that elimination of F₂ from PtF₈ is a strongly exothermic reaction, with a moderate activation barrier. An exothermic decay is also observed for the homolytic bond breaking. Furthermore, our investigations suggest that both decomposition channels of PtF₇ are exothermic. The existence of platinum fluorides higher than PtF₆ is therefore highly unlikely.     

Catalytic roles of the metal ion in the substrate-binding site of coenzyme B12-dependent diol dehydratase

Functions of the metal ion in the substrate-binding site of diol dehydratase are studied on the basis of quantum mechanical/molecular mechanical (QM/MM) calculations. The metal ion directly coordinates to substrate and is essential for structural retention and substrate binding. The metal ion has been originally assigned to the K(+) ion; however, QM/MM computations indicate that Ca(2+) ion is more reasonable as the metal ion because calculated Ca-O distances better fit to the coordination distances in X-ray crystal structures rather than calculated K-O distances. The activation energy for the OH group migration, which is essential in the conversion of diols to corresponding aldehydes, is sensitive to the identity of the metal ion. For example, the spectator OH group of substrate is fully deprotonated by Glu170 in the transition state for the OH group migration in the Ca-contained QM/MM model, and therefore the barrier height is significantly decreased in the model having Ca(2+) ion. On the other hand, the deprotonation of the spectator OH group cannot effectively be triggered by the K(+) ion. Moreover, in the hydrogen recombination, the most energy-demanding step is more favorable in the Ca-contained model. The proposal that the Ca(2+) ion should be involved in the substrate-binding site is consistent with an observed large deuterium kinetic isotope effect of 10, which indicates that C-H bond activation is involved in the rate-determining step. Asp335 is found to have a strong anticatalytic effect on the OH group migration despite its important role in substrate binding. The synergistic interplay of the O-C bond cleavage by Ca(2+) ion and the deprotonation of the spectator OH group by Glu170 is required to overcome the anticatalytic effect of Asp335.     

Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor

The free energy barriers and a mechanism of the oxidation of the amino acid methionine in water and in granulocyte colony-stimulating factor (G-CSF) are analyzed via combined quantum mechanical and molecular mechanical (QM/MM) methods, constrained molecular dynamics, and committor probability calculations. The computed free energy barrier of free methionine amino acid is very close to the measured value (14.7 +/- 1.2 versus 15.5 +/- 0.02 kcal/mol). The reaction coordinate was found to be the difference between the O-O bond of H2O2 and the S-O bond, where the S is the sulfur atom of the methionine residue. It was confirmed by computing the committor probability distribution and the distribution of constrained forces that this coordinate is not coupled to the activation of other degrees of freedom. The computed free energies of the oxidation of methionine residues in G-CSF indicate that the protein environment has insignificant effects on the reaction barriers of oxidation. This result further validates our proposal that the access of solvent to methionine sites, as measured by the two-shell water coordination number, governs the kinetics of the oxidation reaction of methionine groups in a protein molecule. We also found that the number of hydrogen bonds between the distal oxygen of H2O2 and the water molecules near the methionine increases along the reaction coordinate as oxidation progresses, indicating that the charge separation developed during the oxidation by H2O2 is stabilized by specific interactions with water molecules, such as hydrogen bonding.     

Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study

Bacterial peptide deformylase (PDF) represents a novel class of mononuclear iron peptidase, and has an intriguing metal preference different from most other metalloproteases. Using a hybrid density functional theory (B3LYP) QM/MM method, we have theoretically investigated its catalytic mechanism and metal specificity by studying both Fe2+-PDF and Zn2+-PDF. In both forms of PDF, the conserved Glu133 residue is protonated in the reactant complex, and acts as a general acid during the reaction. The initial reaction step is the nucleophilic attack of the metal-bound hydroxide on the carbonyl carbon of the substrate. Our calculations indicate that the metal ion in Fe2+-PDF is always pentacoordinated during the reaction process, while that in Zn2+-PDF is only tetrahedrally coordinated and not bound to the substrate in the reactant complex. This difference in their metal coordination is suggested to account for the lower activity of Zn2+-PDF in comparison with Fe2+-PDF.     

QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue

SB-3CT, (4-phenoxyphenylsulfonyl)methylthiirane, is a potent, mechanism-based inhibitor of the gelatinase sub-class of the matrix metalloproteinase (MMP) family of zinc proteases. The gelatinase MMPs are unusual in that there are several examples where both enantiomers of a racemic inhibitor have comparable inhibitory abilities. SB-3CT is one such example. Here, the inhibition mechanism of the MMP2 gelatinase by the (S)-SB-3CT enantiomer and its oxirane analogue is examined computationally, and compared to the mechanism of (R)-SB-3CT. Inhibition of MMP2 by (R)-SB-3CT was shown previously to involve enzyme-catalyzed C-H deprotonation adjacent to the sulfone, with concomitant opening by β-elimination of the sulfur of the three-membered thiirane ring. Similarly to the R enantiomer, (S)-SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part (46 atoms) and the AMBER force field for the MM part were used to compare the reaction of (S)-SB-3CT and its oxirane analogue in the active site of MMP2 (9208 atoms). These calculations show that the barrier for the proton abstraction coupled ring opening reaction of (S)-SB-3CT in the MMP2 active site is 4.4 kcal/mol lower than its oxirane analogue, and the ring opening reaction energy of (S)-SB-3CT is only 1.6 kcal/mol less exothermic than its oxirane analogue. Calculations also show that the protonation of the ring-opened products by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane, than for the thiolate obtained from the thiirane. In contrast to (R)-SB-3CT and the R-oxirane analogue, the double bonds of the ring-opened products of (S)-SB-3CT and its S-oxirane analogue have the cis-configuration. Vibrational frequency and intrinsic reaction path calculations on a reduced size QM/MM model (2747 atoms) provide additional insight into the mechanism. These calculations yield 5.9 and 6.7 for the deuterium kinetic isotope effect for C-H bond cleavage in the transition state for the R and S enantiomers of SB-3CT, in good agreement with the experimental results.     

How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study

We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg(2+) ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg(2+) ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.     

Why are olefins oxidized by RuO4 under cleavage of the carbon-carbon bond whereas oxidation by OsO4 yields cis-diols?

Quantum chemical calculations using gradient-corrected (B3LYP) density functional theory have been carried out to investigate the mechanism of the oxidative cleavage of alkenes by ruthenium tetraoxide. The initial reaction of the tetraoxide with the olefin occurs via a [3+2] cycloaddition as in the case of osmium tetraoxide. The results clearly show that the bond cleavage does not take place at the primary adduct, but much later in the reaction path. After the formation of the ruthenium(VI)dioxo-2,5-dioxolane, the reaction proceeds with the addition of a second olefin to yield ruthenium(IV)-bis(2,5-dioxolane), which in turn becomes oxidized first to rutheniumoxo(VI)-bis(2,5-dioxolane) 6(Ru) and then to ruthenium(VIII)-dioxo-bis(2,5-dioxolane) 7(Ru). Only in complexes containing the metal center in the formal oxidation state +VIII are low activation barriers for C-C bond cleavage and exothermic formation of carbonyl compounds as products calculated. The lowest activation barrier, DeltaH(++) = 2.5 kcal/mol, is calculated for the C-C bond breaking reaction of 7(Ru) which is predicted as the pivotal intermediate of the oxidation reaction. The calculations of the oxidation reaction with OsO(4) show that those reactions where the oxidation state of the metal increases have larger activation barriers for M = Ru than for M = Os, while reactions which reduce the oxidation state have a lower activation barrier for ruthenium compounds. Also, reactions which increase the oxidation state of the metal are in the case of M = Os more exothermic than for M = Ru. In this work, all important points of the potential energy surface (PES) are reported, and the complete catalytic cycle for the oxidative cleavage of olefins by ruthenium tetraoxide is presented.     

Predicting the coordination geometry for Mg2+ in the p53 DNA-binding domain: insights from computational studies

Zn(2+) in the tumor-suppressor protein p53 DNA-binding domain (DBD) is essential for its structural stability and DNA-binding specificity. Mg(2+) has also been recently reported to bind to the p53DBD and influence its DNA-binding activity. In this contribution, the binding geometry of Mg(2+) in the p53DBD and the mechanism of how Mg(2+) affects its DNA-binding activity were investigated using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Various possible coordination geometries of Mg(2+) binding to histidines (His), cysteines (Cys), and water molecules were studied at the B3LYP/6-311+g** level of theory. The protonation state of Cys and the environment were taken into account to explore the factors governing the coordination geometry. The free energy of the reaction to form the Mg(2+) complexes was estimated, suggesting that the favorable binding mode changes from a four- to six-coordinated geometry as the number of the protonated Cys increases. Furthermore, MD simulations were employed to explore the binding modes of Mg(2+) in the active site of the p53DBD. The simulation results of the Mg(2+) system and the native Zn(2+) system show that the binding affinity of Mg(2+)to the p53DBD is weaker than that of Zn(2+), in agreement with the DFT calculation results and experiments. In addition, the two metal ions are found to make a significant contribution to maintain a favorable orientation for Arg248 to interact with putative DNA, which is critically important to the sequence-specific DNA-binding activity of the p53DBD. However, the effect of Mg(2+) is less marked. Additionally, analysis of the natural bond orbital (NBO) charge transfer reveals that Mg(2+) has a higher net positive charge than Zn(2+), leading to a stronger electrostatic attractive interaction between Mg(2+) and putative DNA. This may partly explain the higher sequence-independent DNA-binding affinity of p53DBD-Mg(2+) compared to p53DBD-Zn(2+) observed in experiment.     

Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction

We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.     

Transition structures, energetics, and nucleus-independent chemical shifts for 6pi electrocyclizations of dienylketenes to cyclohexadienones: a DFT study

6pi electrocyclizations of dienylketenes to 2,4-cyclohexadienones have been investigated at the (U)B3LYP/6-31G level and found to be a favored and exothermic process for most dienylketenes. As evidenced by calculations, dienylketene cyclizations proceed via a pseudopericyclic process. If the terminal double bond of dienylketenes is embedded into a benzenoid-type aryl moiety, the partial or complete loss of aromaticity, as indicated by NICS values, increases the activation barrier and makes the reaction less exothermic or even endothermic. The effect of aromaticity is slightly less pronounced for dienylketenes carrying five-membered heterocyclic aromatic substituents. Slightly distorted planar transition structures have been located for these types of cyclizations. Forming bond lengths in transition structures range from 1.950 to 2.339 A.     

Theoretical studies on farnesyl transferase: evidence for thioether product coordination to the active-site zinc sphere

Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great attention in anticancer research over the last decade. However, despite the major accomplishments in the field, some very pungent questions on the farnesylation mechanism still persist. In this study, the authors have analyzed a mechanistic paradox that arises from the existence of several contradicting and inconclusive experimental evidence regarding the existence of direct coordination between the active-site zinc cation and the thioether from the farnesylated peptide product, which include UV-vis spectroscopy data on a Co(2+)-substituted FTase, two X-ray crystallographic structures of the FTase-product complex, and extended X-ray absorption fine structure results. Using high-level theoretical calculations on two models of different sizes, and QM/MM calculations on the full enzyme, the authors have shown that the farnesylated product is Zn coordinated, and that a subsequent step where this Zn bond is broken is coherent with the available kinetic results. Furthermore, an explanation for the contradicting experimental evidence is suggested.     

Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods and density functional theory (DFT) were used to investigate the initial ring-opening step in the hydrolysis of moxalactam catalyzed by the dizinc L1 beta-lactamase from Stenotrophomonas maltophilia. Anchored at the enzyme active site via direct metal binding as suggested by a recent X-ray structure of an enzyme-product complex (Spencer, J.; et al. J. Am. Chem. Soc. 2005, 127, 14439), the substrate is well aligned with the nucleophilic hydroxide that bridges the two zinc ions. Both QM/MM and DFT results indicate that the addition of the hydroxide nucleophile to the carbonyl carbon in the substrate lactam ring leads to a metastable intermediate via a dominant nucleophilic addition barrier. The potential of mean force obtained by SCC-DFTB/MM simulations and corrected by DFT/MM calculations yields a reaction free energy barrier of 23.5 kcal/mol, in reasonable agreement with the experimental value of 18.5 kcal/mol derived from kcat of 0.15 s(-1). It is further shown that zinc-bound Asp120 plays an important role in aligning the nucleophile, but accepts the hydroxide proton only after the nucleophilic addition. The two zinc ions are found to participate intimately in the catalysis, consistent with the proposed mechanism. In particular, the Zn(1) ion is likely to serve as an "oxyanion hole" in stabilizing the carbonyl oxygen, while the Zn(2) ion acts as an electrophilic catalyst to stabilize the anionic nitrogen leaving group.     

Reduction mechanism in class A methionine sulfoxide reductases: a theoretical chemistry investigation

Ab initio calculations at the B3LYP/6–311 ++G(2df,2p) and B3LYP/6–31G(d) level have been carried out to investigate the reaction mechanism of methionine sulfoxide reductases of class A. These enzymes reduce oxidized methionine in vivo and therefore play an important role in repairing protein damage caused by the oxidative stress. Our calculations have been carried out for a model reaction in a model active site. Several reaction mechanisms have been explored that can roughly be described as (2H⁺ + 2e⁻) or (H⁺ + e⁻). The results suggest that the actual reaction mechanism is of the (2H⁺ + 2e⁻) type corresponding to a more or less asynchronous-concerted double-proton transfer reaction leading to the formation of methionine (dimethylthioether in our model) and a sulfenic acid Cys-SOH. The Michaelis complex would involve one deprotonated Cys and one protonated Glu residues in the active site, this protonation state being mandatory to stabilize the sulfoxide substrate. Then, proton transfer from Glu to the substrate takes place, followed by proton transfer from one Tyr residue and fast reorganization of the system. The overall activation energy barrier is estimated to fall in the range 7–9 kcal/mol, much lower than the predicted barrier in DMSO solution (29.6 kcal/mol) reported before.     

Which one among Zn(II), Co(II), Mn(II), and Fe(II) is the most efficient ion for the methionine aminopeptidase catalyzed reaction?

The catalytic hydrolysis of a methionyl-peptide substrate by a methionine aminopeptidase active site model cluster was investigated at the DF/B3LYP level of theory, in the gas-phase and in the protein environment. Zn(II), Co(II), Mn(II), and Fe(II) transition metals were examined as the potential catalytic metals of this enzyme involved in protein maturation. Two different mechanisms in which Glu204 was present as protonated or deprotonated residue were considered. The energetic profiles show lower barriers as the protonated glutamate is involved. The rate-determining step of the hydrolysis reaction is always the nucleophilic addition of the hydroxide on substrate carbon, followed by less energetically demanding methionine-peptide C-N bond scission. The lowest activation energy is obtained in the case of zinc dication while the other metals show very high energetic barriers, so that methionine aminopeptidase can be in principle recognized as a dizinc enzyme.     

Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations

We present results of a theoretical analysis of the phosphorylation reaction in cAMP-dependent protein kinase using a combined quantum mechanical and molecular mechanics (QM/MM) approach. Detailed analysis of the reaction pathway is provided using a novel QM/MM implementation of the nudged elastic band method, finite temperature fluctuations of the protein environment are taken into account using free energy calculations, and an analysis of hydrogen bond interactions is performed on the basis of calculated frequency shifts. The late transfer of the substrate proton to the conserved aspartate (D166), the activation free energy of 15 kcal/mol, and the slight exothermic (-3 kcal/mol) character of the reaction are all consistent with the experimental data. The near attack conformation of D166 in the reactant state is maintained by interactions with threonine-201, asparagine-177, and most notably by a conserved water molecule serving as a strong structural link between the primary metal ion and the D166. The secondary Mg ion acts as a Lewis acid, attacking the beta-gamma bridging oxygen of ATP. This interaction, along with a strong hydrogen bond between the D166 and the substrate, contributes to the stabilization of the transition state. Lys-168 maintains a hydrogen bond to a transferring phosphoryl group throughout a reaction process. This interaction increases in the product state and contributes to its stabilization.     

New mechanistic insights into the iridium-phosphanooxazoline-catalyzed hydrogenation of unfunctionalized olefins: a DFT and kinetic study

The reaction mechanism of the iridium-phosphanooxazoline-catalyzed hydrogenation of unfunctionalized olefins has been studied by means of density functional theory calculations (B3LYP) and kinetic experiments. The calculations suggest that the reaction involves an unexpected Ir(III)-Ir(V) catalytic cycle facilitated by coordination of a second equivalent of dihydrogen. Thus, in the rate-determining migratory insertion of the substrate alkene into an iridium-hydride bond, simultaneous oxidative addition of the bound dihydrogen occurs. The kinetic data shows that the reaction is first order with respect to hydrogen pressure. This is interpreted in terms of an endergonic coordination of this second equivalent of dihydrogen, although a rate-determining step, in which coordinated solvent is replaced by dihydrogen, could not be ruled out. Furthermore, the reaction was found to be zeroth order with respect to the alkene concentration. This correlates well with the calculated exothermicity of substrate coordination, and the catalyst is thus believed to coordinate an alkene in the resting state. On the basis of the proposed catalytic cycle, calculations were performed on a full-sized system with 88 atoms to assess the appropriateness of the model calculations. These calculations were also used to explain the enantioselectivity exerted by the catalyst.     

Why is tetrazole formation by addition of azide to organic nitriles catalyzed by zinc(II) salts?

The mechanism by which zinc(II) catalyzes the union of an azide ion with organic nitriles to form tetrazoles is investigated by means of density functional theory using the hybrid functional B3LYP. The calculations indicate that coordination of the nitrile to the zinc ion is the dominant factor affecting the catalysis; this coordination substantially lowers the barrier for nucleophilic attack by azide. Relative reaction rates of catalyzed and uncatalyzed tetrazole formation also provide experimental support for this conclusion.