Transition State Symmetry Research Articles

Transition States for Psychrophilic and Mesophilic (R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer at Sub-zero Temperatures.

(R)-3-Hydroxybutyrate dehydrogenase (HBDH) catalyzes the NADH-dependent reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates. The active sites of a pair of cold- and warm-adapted HBDHs are identical except for a single residue, yet kinetics evaluated at -5, 0, and 5 °C show a much higher steady-state rate constant (kcat) for the cold-adapted than for the warm-adapted HBDH. Intriguingly, single-turnover rate constants (kSTO) are strikingly similar between the two orthologues. Psychrophilic HBDH primary deuterium kinetic isotope effects on kcat (Dkcat) and kSTO (DkSTO) decrease at lower temperatures, suggesting more efficient hydride transfer relative to other steps as the temperature decreases. However, mesophilic HBDH Dkcat and DkSTO are generally temperature-independent. The DkSTO data allowed calculation of intrinsic primary deuterium kinetic isotope effects. Intrinsic isotope effects of 4.2 and 3.9 for cold- and warm-adapted HBDH, respectively, at 5 °C, supported by quantum mechanics/molecular mechanics calculations, point to a late transition state for both orthologues. Conversely, intrinsic isotope effects of 5.7 and 3.1 for cold- and warm-adapted HBDH, respectively, at -5 °C indicate the transition state becomes nearly symmetric for the psychrophilic enzyme, but more asymmetric for the mesophilic enzyme. His-to-Asn and Asn-to-His mutations in the psychrophilic and mesophilic HBDH active sites, respectively, swap the single active-site position where these orthologues diverge. At 5 °C, the His-to-Asn mutation in psychrophilic HBDH decreases Dkcat to 3.1, suggesting a decrease in transition-state symmetry, while the His-to-Asn mutation in mesophilic HBDH increases Dkcat to 4.4, indicating an increase in transition-state symmetry. Hence, temperature adaptation and a single divergent active-site residue may influence transition-state geometry in HBDHs.

Unprecedented large solvent (H2O vs D2O) isotope effect in semiconductors photooxidation

AbstractGlucose in water (L2O, L = H or D) at pH = 7 (phosphate buffer) is oxidized in presence of Bi2WO6 and light. An unusually large solvent isotope effects, and 6.8, have been measured using solar light and solar simulator, respectively. These large values come from the contribution of the equilibrium L2O ⇄ L+ + OL− previous to the rate‐limiting step (rls) and the kinetic one (proton transfer) involved at the transition state. The reaction is faster when [L+] increases; therefore, L+ species instead of OL− one participates in the photooxidation. The rls is the 1 e− reduction‐adsorption of H+ on the Bi2WO6 surface (Bi2WO6/Bi2WO6‐H, −0.6 V vs NHE). Subsequently, O2 reduction to L2O, as driving force, occurs at the catalyst conduction band (CB). Linear sweep voltammetry when Bi2WO6 is used as cathode shows two reduction processes: H+/H2 and O2/O2.−. The last one‐electron reduction occurs at −0.2 V vs NHE and the first one at −0.4 V vs NHE. Both show solvent isotope effect, although the are 2.4 and 1.9, respectively, quite smaller than the value obtained in the photooxidation due to the influence of the bias on the transition state symmetry in the first case and through water O2 reduction in the second. Cyclic voltammetry indicates that the reduced and adsorbed H (Bi2WO6‐H2) is oxidized to Bi2WO6‐H at approximately 0.2 V vs NHE. Positive conduction band potential of Bi2WO6 (+0.5 V vs NHE) establishes the difference with other semiconductors where oxidation (L2O/L+,OL.) instead of reduction has been proposed as rls in photooxidation.

Quantum Mechanical Studies for Structures and Energetic of Double Proton Transfer in Biologically Important Hydrogen-bonded Complexes

We have performed quantum mechanical calculations to study the geometries and binding energies of biologically important, cyclic hydrogen-bonded complexes, such as formic acid + <TEX>$H_2O$</TEX>, formamidine + <TEX>$H_2O$</TEX>, formamide + <TEX>$H_2O$</TEX>, formic acid dimer, formamidine dimer, formamide dimer, formic acid + formamide, formic acid + formamidine, formamide + formamidine, and barrier heights for the double proton transfer in these complexes. Various ab initio, density functional theory, multilevel methods have been used. Geometries and energies depend very much on the level of theory. In particular, the transition state symmetry of the proton transfer in formamidine dimer varies greatly depending on the level of theory, so very high level of theory must be used to get any reasonable results.

Group theory and reaction mechanisms: An extension of the mciver-stanton rules

McIver and Stanton's rules concerning the symmetry of transition states have a counterpart in rules concerning the permutation symmetry of single steps in degenerate rearrangements, derivable with the aid of Longuet-Higgins group theory. Examples in organometallic fluxional systems and carbonium ions illustrate the rules; the analysis leads to prediction of hitherto unexplored pathways for rearrangements in ethyl and homotetrahedryl cations.

Jet cooled spectroscopy of H2DO+: Barrier heights and isotope-dependent tunneling dynamics from H3O+ to D3O+

The first high resolution spectroscopic data for jet cooled H2DO+ are reported, specifically via infrared laser direct absorption in the OH stretching region with a slit supersonic jet discharge source. Transitions sampling upper (0-) and lower (0+) tunneling states for both symmetric (nu1+ <-- 0+, nu1- <-- 0-, and nu1- <-- 0+) and antisymmetric (nu3+ <-- 0+ and nu3- <-- 0-) OH stretching bands are observed, where +/- refers to wave function reflection symmetry with respect to the planar umbrella mode transition state. The spectra can be well fitted to a Watson asymmetric top Hamiltonian, revealing band origins and rotational constants for benchmark comparison with high-level ab initio theory. Of particular importance are detection and assignment of the relatively weak band (nu1- <-- 0+) that crosses the inversion tunneling gap, which is optically forbidden in H3O+ or D3O+, but weakly allowed in H2DO+ by lowering of the tunneling transition state symmetry from D(3h) to C(2v). In conjunction with other H2DO+ bands, this permits determination of the tunneling splittings to within spectroscopic precision for each of the ground [40.518(10) cm(-1)], nu1 = 1 [32.666(6) cm(-1)], and nu3 = 1 [25.399(11) cm(-1)] states. A one-dimensional zero-point energy corrected potential along the tunneling coordinate is constructed from high-level ab initio CCSD(T) calculations (AVnZ, n = 3,4,5) and extrapolated to the complete basis set limit to extract tunneling splittings via a vibrationally adiabatic treatment. Perturbative scaling of the potential to match splittings for all four isotopomers permits an experimental estimate of DeltaV0 = 652.9(6) cm(-1) for the tunneling barrier, in good agreement with full six-dimensional ab initio results of Rajamaki, Miani, and Halonen (RMH) [J. Chem. Phys. 118, 10929 (2003)]. (DeltaV0 (RMH) = 650 cm(-1)). The 30%-50% decrease in tunneling splitting observed upon nu1 and nu3 vibrational excitations arises from an increase in OH stretch frequencies at the planar transition state, highlighting the transition between sp2 and sp3 hybridizations of the OHD bonds as a function of inversion bending angle.

Potential Energy Surfaces for Ligand Exchange Reactions of Square Planar Diamagnetic PtY2L2 Complexes:Hydrogen Bond (PtY2L2…L') versus Apical (Y2L2Pt…L') Interaction

The geometrical structures, potential energy surfaces, and energetics for the ligand exchange reactions of tetracoordinated platinum <TEX>$(PtY_2L_2\;:\;Y,\;L=Cl^-,\;OH^-,\;OH_2,\;NH_3)$</TEX> complexes in the ligand-solvent interaction systems were investigated using the ab initio Hartree-Fock (HF) and Density Functional Theory (DFT) methods. The potential energy surfaces for the ligand exchange reactions used for the conversions of <TEX>$(PtCl_4\;+\;H_2O)^{^\ast_\ast}\;to\;[PtCl_3(H_2O)\;+\;Cl^-]$</TEX> and <TEX>$[Pt(NH_3)_2Cl_2\;+\;H_2O]$</TEX><TEX>$[Pt(NH_3)_2Cl_2\;+\;H_2O]$</TEX> to <TEX>$[Pt(NH_3)_2Cl(H_2O)\;+\;Cl^-] $</TEX> were investigated in detail. For these two exchange reactions, the transition states <TEX>$([PtY_2L_2{\cdot}{\cdot}{\cdot}L^\prime])^{^\ast_\ast} $</TEX> correspond to complexes such as <TEX>$(PtCl_4{\cdot}{\cdot}{\cdot}H_2O)^{^\ast_\ast}$</TEX> and <TEX>$[Pt(NH_3)_2Cl_2{\cdot}{\cdot}{\cdot}H_2O]^{^\ast_\ast}$</TEX>, respectively. In the transition state, <TEX>$([PtCl_4{\cdot}{\cdot}{\cdot}H_2O]^{^\ast_\ast}$</TEX> and <TEX>$[Pt(NH_3)_2Cl_2{\cdot}{\cdot}{\cdot}H_2O]]^{^\ast_\ast})$</TEX> have a kind of 6-membered <TEX>$(Pt-Cl{\cdot}{\cdot}{\cdot}HOH{\cdot}{\cdot}{\cdot}Cl)$</TEX> and <TEX>$(Pt-OH{\cdot}{\cdot}{\cdot}Cl{\cdot}{\cdot}{\cdot}HN)$</TEX> interactions, respectively, wherein a central Pt(II) metal directly combines with a leaving <TEX>$Cl^-$</TEX> and an entering <TEX>$H_2O$</TEX>. Simultaneously, the entering <TEX>$H_2O$</TEX> interacts with a leaving <TEX>$Cl^-$</TEX>. No vertical one metal-ligand interactions <TEX>$([PtY_2L_2{\cdot}{\cdot}{\cdot}L^\prime]) $</TEX> are found at the axial positions of the square planar <TEX>$(PtY_2L_2)$</TEX> complexes, which were formed via a vertically associative mechanism leading to <TEX>$D_{3h}$</TEX> or <TEX>$C_{2v}$</TEX>-transition state symmetry. The geometrical structure variations, molecular orbital variations (HOMO and LUMO), and relative stabilities for the ligand exchange processes are also examined quantitatively. Schematic diagrams for the dissociation reactions of {PtCl4(H2O)n(n=2,4)} into {<TEX>$PtCl_3(H_2O)_{(n-2)}\;+\;Cl^-(H_2O)_2$</TEX>} and the binding energies {<TEX>$PtCl_4(H_2O)_n$</TEX>(n = 1-5)} of <TEX>$PtCl_4$</TEX> with water molecules are drawn.

Transition state symmetries and theoretical activation enthalpies for chloride exchange at planar [PdCl 4] 2−

Density functional theory is applied to associatively activated and dissociative chloride exchange on planar [PdCl 4] 2−. It is shown generally that the highest possible transition state symmetry for associative activation is C 2v. However, for [PdCl 5] 3−, the rigorously trigonal bipyramidal (D 3h) geometry has virtually the same energy and geometry. Enthalpic corrections have little effect on the DFT energy barriers although DFT alone predicts dissociation to be preferred due to the more favourable electrostatic interactions. Inclusion of solvation enthalpies establishes associative activation as the lower energy pathway in agreement with experimental assignments for related processes.

Deducing the symmetry operations generated at a transition state

The problem of transition state symmetry determination is investigated. It is shown how the symmetry operations generated at the transition state for an interconversion between two versions of the same (non-planar) structure may be found. We assume that a reaction follows steepest descent paths on either side of the transition state and that there is a single symmetry-equivalent path between the two minima. The representation of point group operations by permutations and permutation—inversions of identical nuclei is used so that the point group of each version is isomorphic to a subgroup of the CNPI group. The operations which relate each version to the other are then cosets in the CNPI group. The symmetry operations unique to the transition state between them are those common to both cosets. The discussion is extended to cover the interconversion of planar structures and single-step paths between labelled-atom enantiomers.

The reactions of ground and excited state sodium atoms with hydrogen halide molecules

The reactions of ground and excited state Na atoms with hydrogen halide (HX) molecules have been studied using the crossed molecular beams method. With both increasing translational and increasing electronic energy, the reactive cross sections increase in the reactions of HCl and HBr. From product angular and velocity distributions detailed center-of-mass information is derived. For the reactions of Na (3 2S 1 2 , 3 2P 1 2 , 4 2D 5 2 , 5 2S 1 2 ) with HCl, the product NaCl is back-scattered with respect to the incoming Na atom in the center-of-mass frame of reference. The reaction of each Na state studied with HCl is direct and proceeds via collinear and near-collinear Na-Cl-H approach geometries. For the Na (3 2P 3 2 ) and Na (4 2D 5 2 ) reactions with HCl the predominant transition state symmetry is 2Σ in a collinear (C ∞ν) Na-Cl-H geometry. This is consistent with the reaction proceeding via electron transfer from the Na atom to the halide atom. Absolute reactive cross sections for each state of Na studied with HCl were determined by comparison with both small and large angle elastic scattering. We were unable to observe Na atoms with over 4 eV of electronic energy react with HF up to collision energies of 13 kcal/mole.

Transition State Theory

1. significant progress with the variational formulation of classical TST, in which the objects of interest are transition 2. the study of quantum analogues of these generalized transition states, which has led to a practical and reliable rate theory for atom-diatom reactions; 3. the development of a quantum TST that avoids the separability ap­ proximation of conventional TST; 4. the use of the TST line of no return idea as an aid in the calculation of reaction rates from individual initial states; 5. the invention of an interpolating theory to connect the TST rate ex­ pressions for direct and complex reactions; 6. the use of variational TST to calculate capture cross sections in ion­ molecule reactions; 7. the resolution of a few questions concerning transition state symmetry.

Group theory and reaction mechanisms: Permutation theoretic prediction and computational support for pseudorotation modes in C2H and C5H rearrangements

AbstractThe McIver–Stanton rules concerning the symmetry of transition states have a counterpart in rules concerning the permutation symmetry of single steps in degenerate rearrangements, derivable with the aid of Longuet–Higgins group theory. The generalized rules are illustrated by the widely studied PX5 polytopal rearrangements. The analysis leads to prediction of hitherto unexplored “pseudorotation” pathways for rearrangements in ethyl and homotetrahedryl cations. CNDO computations of system energies, gradients, and curvatures at critical points on the C2H and C5H surfaces indicate that symmetry‐breaking in keeping with the permutation‐theoretic predictions is a key feature of the low‐energy rearrangements of these systems. In particular, computation indicates that the C2v “classical” homotetrahedral cation corresponds to an energy maximum rather than an energy minimum, or a transition state.

13C kinetic isotope effects and reaction coordinate motions in transition states for SN2 displacement reactions

Reaction coordinate motions and 13C kinetic isotope effects at 25 °C have been calculated for the SN2 reactions of methyl iodide with iodide, cyanide, and chloride ions and for the SN2 reaction of benzyl bromide with hydroxide ion using transition state models characterized by single interaction force constant, F12, between the bond being formed and the bond being broken. The isotope effect calculations show that the dependence of calculated 13C isotope effects on transition state symmetry found by Willi and Sims etal. holds true for reaction barriers corresponding to small values of νL, while the symmetry dependence observed by Bron holds true for barriers corresponding to large values of νL.νL was also found to have a strong influence on the reaction coordinate motions of the transition states. In particular, for the methyl iodide reactions an increase in νL increases the distortion of the methyl group in the direction expected for a classical SN2 reaction. Finally, reaction coordinate motions were used to show that the model proposed by Bron for the borderline region between SN1 and SN2 reaction mechanisms predicts an increase in the 13C kinetic isotope effect with decreasing total bond order and not the decrease suggested by Bron.

On simple saddle points of a potential surface, the conservation of nuclear symmetry along paths of steepest descent, and the symmetry of transition states

We show that if the transition state of a chemical reaction is a simple saddle point of the potential surface linked directly with reactants and products by paths of steepest descent, then the symmetry of the transition state is limited to the joint symmetry of reactant and product, unless reactant and product are physically indistinguishable and themselves symmetry related, in which case the transition state may have those additional symmetries that interchange reactant and product. We outline some of the general consequences of this symmetry restriction on transition states.

The carbanion mechanism of olefin-forming elimination. Part VII. The isotope effect maximum in the dehydrochlorination of 2,2,2-trichloro-1,1-bis-(p-chlorophenyl)ethane by various bases in alcholic solvents

When the E1cB dehydrochlorination reactions of Ar2CH·CCl3 and Ar2CD·CCl3(Ar =p-ClC6H4) are induced by a series of bases in ethanol ranging in strength from PhS– to OEt–, a maximum in KH/KD is observed for phenoxide as base. The kinetics of the phenoxide-induced reactions are re-examined using conditions under which buffering of the reaction solutions is ensured. The maximum is found to be real. An Arrhenius equation study of the reactions, and the reactions of PhS–, OMe–(in McOH), and OEt– with these substrates fails to reveal a significant contribution from proton tunnelling to KH/KD values. It is proposed that the maximum is caused by variations in transition state symmetry.

Solvent dependence of the primary deuterium kinetic isotope effect in the sodium hydroxide-catalysed E2 elimination of hydrogen bromide from p-acetyl- and p-nitro-phenethyl bromide

Rate constants have been determined from the NaOH-catalysed 1,2-elimination of HBr from p-acetyl- and p-nitro-phenethyl bromide over a range of dimethyl sulphoxide concentrations. The calculated K2H/K2D ratios show no dependence on the para-substituent or the dimethyl sulphoxide concentration except for p-nitrophenethyl bromide at 59.7 and 69.7 mole %. The change in the isotope effect for the p-nitro-compound cannot be satisfactorily explained in terms of a change in transition-state symmetry. The previously reported substituent-induced maximum in the isotope effect for phenethyl bromides is shown to be due to a specific solvent effect rather than indicative of a ‘Westheimer’ maximum. The implication of the overall lack of variation is briefly discussed.

Indices of transition state symmetry in proton-transfer reactions. Kinetic isotope effects and Bronested's .beta. in base-catalyzed diazo-coupling reactions

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIndices of transition state symmetry in proton-transfer reactions. Kinetic isotope effects and Bronested's .beta. in base-catalyzed diazo-coupling reactionsSamir B. Hanna, Carlo Jermini, Hana Loewenschuss, and H. ZollingerCite this: J. Am. Chem. Soc. 1974, 96, 23, 7222–7228Publication Date (Print):November 1, 1974Publication History Published online1 May 2002Published inissue 1 November 1974https://doi.org/10.1021/ja00830a009RIGHTS & PERMISSIONSArticle Views165Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (803 KB) Get e-Alerts Get e-Alerts

Heteroaromatic hydrogen exchange reactions. Part VI. Isotope effect for the acid-catalysed exchange of some 3-2H1- and 3-3H1-indoles

Rates of deuterium and tritium displacement at 25 °C from the 3-position of indole, 5-methoxyindole, and 5-cyanoindole are reported for various aqueous acetic acid buffer solutions, together with data for indole in aqueous pyridine buffers and for indole and 5-cyanoindole in dilute HCl. Deuterium is displaced more readily than tritium throughout, and the incidence of general acid catalysis suggests a common A–SE2 exchange mechanism. Isotopic rate ratios computed from the experimental data for this pathway are substantial (kH/kD= 4·5–6·3) and show little systematic variation with the reactivity of either the substrate or the acid catalyst. Comparison with earlier data shows that the indole substrates are not exceptional in this respect and the size of the kinetic isotope effect appears to be an insensitive, if not unsatisfactory, index of transition state symmetry for aromatic hydrogen exchange reactions. Bronsted exponents for H3O+– and HOAc- catalysed exchange of these indoles are β= 0·67 and β= 0·75, respectively. Both are significantly larger than the Bronsted exponent obtained by the variation of the acid catalyst for exchange of 2-methylindole.

The ordering of carbon–hydrogen bond strengths using isotope effects

Variations in the tritium isotope effects in the radical addition of R1SH to R2R3CCH2 are interpreted in terms of the transition state symmetry, measured by the difference in bond strengths to hydrogen in the initial state (R1S–H) and the final state (H–CR2R3CH2SR1).

Statistical factors and the symmetry of transition states

The relative merits of statistical factors and symmetry numbers in transition state theory are discussed in relation to potential energy surfaces with valley bifurcations. Conditions for the applicability of the two methods are considered in terms of the details of the motion at the bifurcation, and some examples are discussed.

Struktur und reaktivität aliphatischer diazoverbindungen—XVIII

The rate of the acid-catalysed hydrolysis of p-nitrophenyl-diazomethane has been measured in dioxan-water/HClO4. As indicated by the solvent deuterium isotope effect kH/kD = 3·76 and the general acid catalysis in acetic acid-sodium acetate buffer solutions, the decomposition proceeds by rate-controlling protonation (A-SE2 mechanism). These results are not in accordance with the recent findings of the A-2 hydrolyses of primary and of the A-SE2 hydrolyses of secondary diazo alkanes and α-diazocarbonyl compounds. The stability toward acids is increased by substitution at the diazo C atom of IIIa. In the reaction series IIIa–g the rate of hydrolysis at 20° decreases from k2 = 82.10−1 1.mol−1.s−1 for IIIa to k2 = 11·3.10−5 1.mol−1.s−1 in the case of IIIg. A variation of the mechanism of hydrolysis was not observed. The plot of the logarithms of the rate constants k2 for the acid-catalysed hydrolysis of IIIb–g vs σ*, the Taft substituent constant, has been found to be linear with a slope ϱ* = − 1·869. With decreasing reactivity also the solvent isotope effect kH/kD decreases from a value of 3·76 in the case of IIIa to a range between 1·55 and 1·95 for IIId–g. An approximately linear relationship is indicated between the magnitude of kH/kD and the reactivity lg k2 (Fig 1). This correlation shows the theoretically expected substituent effects on transition-state symmetry for rate-determining proton-transfer reactions.