Post-reactive Complexes Research Articles

Testing the performance of density functionals for the calculation of energetic properties of complex-forming radical-molecule reactions

The performance of some popular and some more recent density functional methods for the calculation of energies of stationary points on the potential surfaces of radical-molecule reactions was examined. The functionals studied are B3-LYP, BH&H, BH&H-LYP, MPW1K, MPWB1K, TPSS, TPSSh, BB1K, M05 and M05-2X, in conjunction with nine different AO basis sets. The reaction energies, barrier heights and the relative energies of the pre-and post-reaction complexes were compared with those obtained at the CCSD(T)/CBS limit for the reactions of OH radicals with HOOH and CH3OOH. Very poor barrier heights are provided by the B3-LYP, TPSS and TPSSh functionals. The best overall performance was obtained with the BB1K, MPW1K and MPWB1K functionals. In these reactions all of the studied functionals provide converged results only if they are used with large basis sets like aug-cc-pVTZ and def2-TZVP. The data show that before relying on a functional for a specific reaction, it is desirable to make some test calculations on the performance. The same functional can predict some relative energies very well and some others very poorly even in systems including chemically similar reactants.

Quantum-chemical study on the reaction of phenyl isocyanate with linear methanol associates. Addition at the C=N bond

Quantum-chemical calculations at the B3LYP/6-311++G(df,p) level of theory showed that reactions of phenyl isocyanate with methanol associates involve formation of pre-and post-reaction complexes. The reactions proceed through late asymmetric cyclic transition states. The height of the energy barrier decreases as the degree of association of the alcohol increases. The relative change in the Gibbs energy in the reaction of phenyl isocyanate with methanol also becomes smaller as the degree of alcohol association increases.

Facile SN2 Reaction in Protic Solvent: Quantum Chemical Analysis

We study the effects of protic solvent (water, methanol, ethanol, and tert-butyl alcohol) and cation (Na+, K+, Cs+) on the unsymmetrical SN2 reaction X- + RY --> RX + Y- (X = F, Br; R = CH3,C3H7;Y = Cl, OMs). We describe a series of calculations for the S(N)2 reaction mechanism under the influence of cation and protic solvent, presenting the structures of pre- and postreaction complexes and transition states and the magnitude of the activation barrier. An interesting mechanism is proposed, in which the protic solvent molecules that are shielded from the nucleophile by the intervening cation act as a Lewis base to reduce the unfavorable Coulombic influence of the cation on the nucleophile. We predict that the reaction barrier for the S(N)2 reaction is significantly lowered by the cooperative effects of cation and protic solvent. We show that the cation and protic solvent, each of which has been considered to retard the SN2 reactivity of the nucleophile, can accelerate the reaction tremendously when they interact with the fluoride ion in an intricate, combined fashion. This alternative S(N)2 mechanism is discussed in relation to the recently observed phenomenal efficiency of fluorination in tert-alcohol media [Kim, D. W.; et al. J. Am. Chem. Soc. 2006, 128, 16394].

Dual role of the RNA substrate in selectivity and catalysis by terminal uridylyl transferases

Terminal RNA uridylyltransferases (TUTases) catalyze template-independent UMP addition to the 3' hydroxyl of RNA. TUTases belong to the DNA polymerase beta superfamily of nucleotidyltransferases that share a conserved catalytic domain bearing three metal-binding carboxylate residues. We have previously determined crystal structures of the UTP-bound and apo forms of the minimal trypanosomal TUTase, TbTUT4, which is composed solely of the N-terminal catalytic and C-terminal base-recognition domains. Here we report crystal structures of TbTUT4 with bound CTP, GTP, and ATP, demonstrating nearly perfect superposition of the triphosphate moieties with that of the UTP substrate. Consequently, at physiological nucleoside 5'-triphosphate concentrations, the protein-uracil base interactions alone are not sufficient to confer UTP selectivity. To resolve this ambiguity, we determined the crystal structure of a prereaction ternary complex composed of UTP, TbTUT4, and UMP, which mimics an RNA substrate, and the postreaction complex of TbTUT4 with UpU dinucleotide. The UMP pyrimidine ring stacks against the uracil base of the bound UTP, which on its other face also stacks with an essential tyrosine. In contrast, the different orientation of the purine bases observed in cocrystals with ATP and GTP prevents this triple stacking, precluding productive binding of the RNA. The 3' hydroxyl of the bound UMP is poised for in-line nucleophilic attack while contributing to the formation of a binding site for a second catalytic metal ion. We propose a dual role for RNA substrates in TUTase-catalyzed reactions: contribution to selective incorporation of the cognate nucleoside and shaping of the catalytic metal binding site.

The activation of C-H bonds in C1-C3 alkanes by zirconium(III,IV) and titanium(III,IV) hydrides immobilized on the surface of SiO2: a density functional theory study

Model reactions of the (≡Si-O-)3MIVH (1), (≡Si-O-)2MIVH2 (2), and (≡Si-O-)2MIIIH (3) hydrides, where M = Ti and Zr, immobilized on the surface of silica with methane and propane were studied by the density functional theory with the PBE functional. The reactions involved the breaking of C-H alkane bonds and the formation of the (≡Si-O-)3MR, (≡Si-O-)2M(H)R, and (≡Si-O-)2MR products (R = Me, n-Pr, and i-Pr), respectively. Reactions with the participation of 1 and 2 were found to occur as bimolecular processes without the formation of agostic-type prereaction complexes. With 3, the reaction was accompanied by the formation of stable prereaction and postreaction complexes. The conclusion was drawn that dihydrides 2 and trivalent metal hydrides 3 were much more reactive with respect to alkane C-H bonds than monohydrides 1. All the systems studied were characterized by low reaction regioselectivities.

Site specificity of α‐H abstraction reaction among secondary structure motif—Anab initiostudy

The initial step of protein oxidation is studied through alpha-H abstraction by an OH radical with various secondary structure motifs of proteins. It is found that there exist preferential alpha-Hs in this kind of abstractions. The typical abstraction mechanism involves three steps: forming a pre-reactive complex before abstraction, the abstraction reaction, and the H(2)O detachment from a post-reactive complex to form the product, C(alpha)-center radical. Using the stability of the pre-reactive complex and the reaction barrier, we provide some explanation for this site preference. The feasibility of alpha-H abstraction by OH radical depends not only on the types of secondary structure, but also on the reaction condition, such as in aqueous or in gas phase. Moreover, the reactivity of the abstraction also depends on the location of alpha-H in the secondary structure motifs. The preferential alpha-Hs to be abstracted in beta-sheet are those immediate to the amide or carbonyl group, and without involving hydrogen bonding, whereas in reverse turns, the preferential alpha-Hs are near the C-terminal of type I and near the N-terminal of type II. In general, the alpha-Hs in alpha-helix are more difficult to be abstracted than those in beta-sheet and polypeptide in linear form. It is consistent with the trend of their bond dissociation energies. Our theoretical rate constant of N-acetyldiglycin-methylamide (Ac(Gly)(2)NHCH(3)) in aqueous solution (6.75 x 10(8) M(-1) s(-1)) is close to the experimental observation of N-acetyldiglycinamide (Ac(Gly)(2)NH(2)) (8.6 x 10(8) M(-1) s(-1)).

Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism

The number of metal ions required for phosphoryl transfer in restriction endonucleases is still an unresolved question in molecular biology. The two Ca(2+) and Mn(2+) ions observed in the pre- and post-reactive complexes of BamHI conform to the classical two-metal ion choreography. We probed the Mg(2+) cofactor positions at the active site of BamHI by molecular dynamics simulations with one and two metal ions present and identified several catalytically relevant sites. These can mark the pathway of a single ion during catalysis, suggesting its critical role, while a regulatory function is proposed for a possible second ion.

Isotope Labeling and Theoretical Study of the Formation of a 3* Ions from Protonated Tetraglycine

Extensive 13C, 15N, and 2H labeling of tetraglycine was used to investigate the b3+ --> a3* reaction during low-energy collision-induced dissociation (CID) in a quadrupole ion-trap mass spectrometer. The patterns observed with respect to the retention or elimination of the isotope labels demonstrate that the reaction pathway involves elimination of CO and NH3. The ammonia molecule includes 2 H atoms from amide or amino positions, and one from an alpha-carbon position. The loss of NH3 does not involve elimination of the N-terminal amino group but, instead, the N atom of the presumed oxazolone ring in the b3+ ion. The CO molecule eliminated is the carbonyl group of the same oxazolone ring, and the alpha-carbon H atom is transferred from the amino acid adjacent to the oxazolone ring. Quantum chemical calculations indicate a multistep reaction cascade involving CO loss on the b3 --> a3 pathway and loss of NH=CH2 from the a3 ion to form b2. In the postreaction complex of b2 and NH=CH2, the latter can be attacked by the N-terminal amino group of the former. The product of this attack, an isomerized a3 ion, can eliminate NH3 from its N-terminus to form a3*. Calculations suggest that the ammonia and a3* species can form various ion-molecule complexes, and NH3 can initiate relay-type mobilization of the oxazolone H atoms from alpha-carbon positions to form a new oxazolone isomer. This multiple-step reaction scheme clearly explains the isotope labeling results, including unexpected scrambling of H atoms from alpha-carbon positions.

DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion

HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G↓CGC in DNA. We report three structures of HinP1I–DNA complexes: in the presence of Ca2+ (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg2+ (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca2+ or Mg2+) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.

Theoretical kinetic study of the CH 3Br + OH atmospheric system

Ab initio calculations were conducted for both reaction pathways of the CH 3Br and OH system. Geometry optimization and vibrational frequencies analysis were performed for reactants, pre-reaction complex, transition states, post-reaction complex and products at the MP2(full)/6-311+G(d,p), MP2(full)/6-311+G(3df,2pd) and MP2(full)/cc-pVTZ levels of theory. Energetic results were further refined by CCSD(T,full) calculations, using optimized geometric parameters of the MP2(full)/cc-pVTZ level, i.e., CCSD(T,full)/cc-pVTZ//MP2(full)/cc-pVTZ. Based on MP2(full)/cc-pVTZ and CCSD(T,full)/cc-pVTZ//MP2(full)/cc-pVTZ data, rate constants were deduced in the 200–2000 K temperature range, using conventional transition state theory and Wigner tunneling correction. Calculated rate constants, including tunneling corrections, were found to be in excellent agreement with experimental results.

H-atom abstraction dynamics of reactions between Cl atoms and heterocyclic organic molecules

The HCl(v' = 0, J') rotational state distributions produced in the photoinitiated reactions of ground spin-orbit state Cl(2P3/2) atoms with the organic heterocycles oxirane (c-C2H4O), thiirane (c-C2H4S) and oxetane (c-C3H6O) have been measured using the technique of 2 + 1 resonance-enhanced multiphoton ionization in a time-of-flight mass spectrometer. In contrast to previous studies of H-atom abstraction dynamics by Cl atoms with linear functionalized molecules, the nascent HCl(v' = 0, J') products of the reactions of the three-membered heterocycles oxirane and thiirane are formed rotationally cold, with mean rotational energies <Erot> of (0.28 ± 0.02) kcal mol-1 and (0.31 ± 0.02) kcal mol-1, respectively. The reaction of Cl atoms with the four-membered heterocycle oxetane, however, results in more rotationally excited HCl(v' = 0, J') products for which <Erot> = (0.78 ± 0.03) kcal mol-1. Ab initio calculations were performed at the G2//MP2/6-311G(d,p) level to characterize molecular complexes and transition states on the reactive pathways. In all cases, the reactions were calculated to be barrierless, and weakly bound pre- and post-reaction complexes were located on the potential energy surfaces. The observed distributions and calculated reaction profiles are compared with previous studies of the reactions of Cl atoms with linear functionalized organic molecules and the consequences of the constrained molecular geometry on the HCl(v' = 0, J') rotational distribution discussed in terms of the dipole-dipole interaction model proposed previously.

High-resolution structure ofmyo-inositol monophosphatase, the putative target of lithium therapy

Inositol monophosphatase is a key enzyme of the phosphatidylinositol signalling pathway and the putative target of the mood-stabilizing drug lithium. The crystal structure of bovine inositol monophosphatase has been determined at 1.4 A resolution in complex with the physiological magnesium ion ligands. Three magnesium ions are octahedrally coordinated at the active site of each of the two subunits of the inositol monophosphatase dimer and a detailed three-metal mechanism is proposed. Ligands to the three metals include the side chains of Glu70, Asp90, Asp93 and Asp220, the backbone carbonyl group of Ile92 and several solvent molecules, including the proposed nucleophilic water molecule (W1) ligated by both Mg-1 and Mg-3. Modelling of the phosphate moiety of inositol monophosphate to superpose the axial phosphate O atoms onto three active-site water molecules orientates the phosphoester bond for in-line attack by the nucleophilic water which is activated by Thr95. Modelling of the pentacoordinate transition state suggests that the 6-OH group of the inositol moiety stabilizes the developing negative charge by hydrogen bonding to a phosphate O atom. Modelling of the post-reaction complex suggests a role for a second water molecule (W2) ligated by Mg-2 and Asp220 in protonating the departing inositolate. This second water molecule is absent in related structures in which lithium is bound at site 2, providing a rationale for enzyme inhibition by this simple monovalent cation. The higher resolution structural information on the active site of inositol monophosphatase will facilitate the design of substrate-based inhibitors and aid in the development of better therapeutic agents for bipolar disorder (manic depression).

Quantum dynamics of gas-phase SN2 reactions.

Understanding the state-resolved dynamics of elementary chemical reactions involving polyatomic molecules, such as the well-known reaction mechanism of nucleophilic bimolecular substitution (SN2), is one of the principal goals in chemistry. In this Review, the progress in the quantum mechanical treatment of SN2 reactions in the gas phase is reviewed. The potential energy profile of this class of reactions is characterized by two relatively deep wells, which correspond to pre- and post-reaction chargedipole complexes. As a consequence, the complex-forming reaction is dominated by Feshbach resonances. Calculations in the energetic continuum constitute a major challenge because the high density of resonance states imposes considerable requirements on the convergence and the energetic resolution of the scattering data. However, the effort is rewarding because new insights into the details of multimode quantum dynamics of elementary chemical reactions can be obtained.

DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites.

Four crystal structures of EcoRV endonuclease mutants K92A and K38A provide new insight into the mechanism of DNA bending and the structural basis for metal-dependent phosphodiester bond cleavage. The removal of a key active site positive charge in the uncleaved K92A-DNA-M(2+) substrate complex results in binding of a sodium ion in the position of the amine nitrogen, suggesting a key role for a positive charge at this position in stabilizing the sharp DNA bend prior to cleavage. By contrast, two structures of K38A cocrystallized with DNA and Mn(2+) ions in different lattice environments reveal cleaved product complexes featuring a common, novel conformation of the scissile phosphate group as compared to all previous EcoRV structures. In these structures, the released 5'-phosphate and 3'-OH groups remain in close juxtaposition with each other and with two Mn(2+) ions that bridge the conserved active site carboxylates. The scissile phosphates are found midway between their positions in the prereactive substrate and postreactive product complexes of the wild-type enzyme. Mn(2+) ions occupy two of the three sites previously described in the prereactive complexes and are plausibly positioned to generate the nucleophilic hydroxide ion, to compensate for the incipient additional negative charge in the transition state, and to ionize a second water for protonation of the 3'-oxyanion. Reconciliation of these findings with earlier X-ray and fluorescence studies suggests a novel mechanism in which a single initially bound metal ion in a third distinct site undergoes a shift in position together with movement of the scissile phosphate deeper into the active site cleft. This reconfigures the local environment to permit binding of the second metal ion followed by movement toward the pentacovalent transition state. The new mechanism suggested here embodies key features of previously proposed two- and three-metal catalytic models, and offers a view of the stereochemical pathway that integrates much of the copious structural and functional data that are available from exhaustive studies in many laboratories.

Theoretical study of the reaction of the ethynyl radical with ammonia (C2H + NH3): hydrogen abstraction versus condensation

Portions of the potential energy surface (PES) related to the reaction between the ethynyl radical and ammonia (C2H + NH3) have been investigated in detail using both MO and DFT methods up to geometry optimizations using the coupled-cluster theory with large basis sets. Several (C2H4N) intermediates and transition structures for unimolecular rearrangements between them have been characterized. Calculations at the CCSD(T)/6-311++G(3df,2p) + ZPE level show that the C2H + NH3 reaction has two main entrance channels: H-abstraction and condensation. The relative energies (kcal mol−1) along the H-abstraction pathway are as follows: 1 C2H + NH3 (0) → pre-reaction complex CO2 (−2.9) → TS (−1.8) → post-reaction complex CO3 (−28.4) → HCCH + NH2 (−26.6). This channel thus starts by formation of a weak complex HCC…H3N, which after H-atom transfer gives rise to another weak complex between the products, HCCH⋯NH2. The energies (kcal mol−1) along the condensation pathway are: 1 C2H + NH3 (0) → pre-association complex CO1 (−6.1) → TS (−3.0) → adduct HCC–NH3 (−7.6) → TS (4.3) → H2N–CCH + H (−14.2). Although both complex CO1 and primary adduct HCC–NH3 are slightly more stable than CO2 and CO3, the transition structure for conversion of the adduct has a substantially higher energy than the reactants and is fairly rigid, whereas the transition state for H-abstraction lies below the reactant limit and is rather loose. Therefore, H-abstraction is calculated to be clearly favored over condensation at all temperatures. The predicted barrier-free main channel is consistent with recent experimental results showing the title reaction to be a fast process exhibiting a negative temperature dependence. In view of the small energy barrier related to the novel condensation pathway, it might contribute at high temperatures in a significant way to the products formation.

Some difficulties in computing BSSE-corrected potential surfaces of chemical reactions

We performed a theoretical and numerical analysis of the different `counterpoise correction' (CP) schemes potentially applicable to correct for the basis set superposition error (BSSE) in the neighborhood of transition structures of chemical reactions. The analysis proved that neither of them is satisfactory: all CP versions result in either discontinuous potential surfaces or yield different energies for the same species in different reactions. Standard CP correction is unavoidable and satisfactory when loosely bound pre- or post-reaction complexes are studied. For transition structures, however, doing no correction is better than any available CP method.

Quantum dynamical study of the Cl-+CH3Br SN2 reaction

H. Wang, E. M. Goldfield and W. L. Hase, J. Chem. Soc., Faraday Trans., 1997, 93, 737 DOI: 10.1039/A606061G

Reaction path Hamiltonian analysis of the dynamics for Cl− + CH3Br → ClCH3 + Br− SN2 nucleophilic substitution

Abstract Coupling terms in the reaction path Hamiltonian (RPH) provide a qualitative interpretation of the non-statistical effects observed in classical trajectory simulations and experiments for the Cl− + CH3Br → ClCH3 + Br− SN2 nucleophilic substitution reaction. The small couplings between the Cl− + CH3Br relative translational, which is the reaction coordinate as the reactants collide, and the CH3Br vibrational modes explain why translation to vibration (T → V) energy transfer is unimportant for Cl− ⋯CH3Br complex formation and, instead, the complex is formed by T → R energy transfer. A large coupling term between the ClCBr symmetric stretch and the reaction coordinate leads to a large reaction path curvature at regions along the reaction path separating the central barrier and the pre- and post-reaction complexes. Such sharp values for the curvature can trap trajectories in the vicinity of the central barrier, which is consistent with the central barrier recrossings observed in classical trajectory simulations. Because of singularities in the RPH it is difficult to use it in classical trajectory simulations. Numerical difficulties in evaluating the long-time flux-flux autocorrelation function for the RPH precludes using this approach for calculating the quantum mechanical rate constant for Cl− + CH3Br SN2 nucleophilic substitution. Also, since the RPH does not include overall rotation and rotational/vibrational coupling and assumes a quadratic expansion for displacements away from the reaction path, this Hamiltonian may not give an accurate quantum mechanical rate constant even if a converged flux-flux autocorrelation function could be evaluated.