The need for enzymatic steering in abietic acid biosynthesis: gas-phase chemical dynamics simulations of carbocation rearrangements on a bifurcating potential energy surface.

Abietic acid, a constituent of pine resin, is naturally derived from abietadiene --a process that requires four enzymes: one (abietadiene synthase) for conversion of the acyclic, achiral geranylgeranyl diphosphate to the polycyclic, chiral abietadiene (a complex process involving the copalyl diphosphate intermediate) and then three to oxidize a single methyl group of abietadiene to the corresponding carboxylic acid. In previous work (Nature Chem.2009, 1, 384), electronic structure calculations on carbocation rearrangements leading to abietadienyl cation revealed an interesting potential energy surface with a bifurcating reaction pathway (two transition-state structures connected directly with no intervening minimum), which links two products--one natural and one not yet isolated from Nature. Herein we describe direct dynamics simulations of the key step in the formation of abietadiene (in the gas phase and in the absence of the enzyme). The simulations reveal that abietadiene synthase must intervene in order to produce abietadiene selectively, in essence steering this reaction to avoid the generation of byproducts with different molecular architectures.

[1]  R. Croteau,et al.  Cyclization Enzymes in the Biosynthesis of Monoterpenes, Sesquiterpenes, and Diterpenes , 2000 .

[2]  Michael Mccoy TALL (OIL) TALE OF PINE CHEMICALS: Hercules is bailing out, but other producers say they are in it for the long term , 2000 .

[3]  Krishnan Raghavachari,et al.  Assessment of Gaussian-3 and Density Functional Theories for Enthalpies of Formation of C1−C16 Alkanes† , 2000 .

[4]  D. Christianson Unearthing the roots of the terpenome. , 2008, Current opinion in chemical biology.

[5]  Donald G. Truhlar,et al.  Small Representative Benchmarks for Thermochemical Calculations , 2003 .

[6]  Donald G. Truhlar,et al.  Adiabatic connection for kinetics , 2000 .

[7]  B. Rabinovitch,et al.  Thermal Unimolecular Geometric and Structural Isomerization of 1,2-Dideuterio-3-methylcyclopropane , 1964 .

[8]  K. Houk,et al.  Dynamics of 1,3-dipolar cycloadditions: energy partitioning of reactants and quantitation of synchronicity. , 2010, Journal of the American Chemical Society.

[9]  D. A. Dougherty,et al.  The Cationminus signpi Interaction. , 1997, Chemical reviews.

[10]  Clémence Corminboeuf,et al.  Systematic errors in computed alkane energies using B3LYP and other popular DFT functionals. , 2006, Organic letters.

[11]  R. Peters,et al.  Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. , 2002, Journal of the American Chemical Society.

[12]  Donald G. Truhlar,et al.  Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics , 2004 .

[13]  C. Musgrave,et al.  Prediction of transition state barriers and enthalpies of reaction by a new hybrid density-functional approximation , 2001 .

[14]  Upakarasamy Lourderaj,et al.  A direct dynamics trajectory study of F- + CH(3)OOH reactive collisions reveals a major non-IRC reaction path. , 2007, Journal of the American Chemical Society.

[15]  Gilles H. Peslherbe,et al.  Monte Carlo Sampling for Classical Trajectory Simulations , 2007 .

[16]  M. Plesset,et al.  Note on an Approximation Treatment for Many-Electron Systems , 1934 .

[17]  R. Croteau,et al.  Diterpenoid resin acid biosynthesis in conifers: enzymatic cyclization of geranylgeranyl pyrophosphate to abietadiene, the precursor of abietic acid. , 1994, Archives of biochemistry and biophysics.

[18]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[19]  D. Major,et al.  Challenges posed to bornyl diphosphate synthase: diverging reaction mechanisms in monoterpenes. , 2010, Journal of the American Chemical Society.

[20]  R. Peters,et al.  Stereochemistry of the cyclization-rearrangement of (+)-copalyl diphosphate to (-)-abietadiene catalyzed by recombinant abietadiene synthase from Abies grandis. , 2000, Organic letters.

[21]  Valerije Vrček,et al.  Quantum Chemical Study of Degenerate Hydride Shifts in Acyclic Tertiary Carbocations , 2002 .

[22]  D. Wales Potential energy surfaces and coordinate dependence , 2000 .

[23]  D. Tantillo,et al.  Quantum chemical dissection of the classic terpinyl/pinyl/bornyl/camphyl cation conundrum-the role of pyrophosphate in manipulating pathways to monoterpenes. , 2010, Organic & biomolecular chemistry.

[24]  Kevin E. Riley,et al.  Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties. , 2007, Journal of chemical theory and computation.

[25]  D. Tantillo The carbocation continuum in terpene biosynthesis--where are the secondary cations? , 2010, Chemical Society reviews.

[26]  J. Sühnel,et al.  C-h⋯π-interactions in proteins , 2001 .

[27]  Donald G Truhlar,et al.  Representative Benchmark Suites for Barrier Heights of Diverse Reaction Types and Assessment of Electronic Structure Methods for Thermochemical Kinetics. , 2007, Journal of chemical theory and computation.

[28]  D. Tantillo,et al.  Consequences of conformational preorganization in sesquiterpene biosynthesis: theoretical studies on the formation of the bisabolene, curcumene, acoradiene, zizaene, cedrene, duprezianene, and sesquithuriferol sesquiterpenes. , 2009, Journal of the American Chemical Society.

[29]  William L. Hase,et al.  DIRECT DYNAMICS SIMULATIONS OF REACTIVE SYSTEMS , 1998 .

[30]  Klaus Ruedenberg,et al.  Bifurcations and transition states , 1986 .

[31]  Andrew G. Leach,et al.  Mechanism of ene reactions of singlet oxygen. A two-step no-intermediate mechanism. , 2003, Journal of the American Chemical Society.

[32]  S. Grimme Seemingly simple stereoelectronic effects in alkane isomers and the implications for Kohn-Sham density functional theory. , 2006, Angewandte Chemie.

[33]  David Feller The role of databases in support of computational chemistry calculations , 1996 .

[34]  Dean J Tantillo,et al.  Theoretical studies on farnesyl cation cyclization: pathways to pentalenene. , 2006, Journal of the American Chemical Society.

[35]  Steven E Wheeler,et al.  Integration Grid Errors for Meta-GGA-Predicted Reaction Energies: Origin of Grid Errors for the M06 Suite of Functionals. , 2010, Journal of chemical theory and computation.

[36]  M. Head‐Gordon,et al.  A fifth-order perturbation comparison of electron correlation theories , 1989 .

[37]  Kazumasa Honda,et al.  The Magnitude of the CH/π Interaction between Benzene and Some Model Hydrocarbons , 2000 .

[38]  A. Becke A New Mixing of Hartree-Fock and Local Density-Functional Theories , 1993 .

[39]  M. Dewar Multibond reactions cannot normally be synchronous , 1984 .

[40]  D. Cane Enzymic formation of sesquiterpenes , 1990 .

[41]  Julian Tirado-Rives,et al.  Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules. , 2008, Journal of chemical theory and computation.

[42]  Matthew D. Wodrich,et al.  The concept of protobranching and its many paradigm shifting implications for energy evaluations. , 2007, Chemistry.

[43]  Dean J Tantillo,et al.  Computational studies on biosynthetic carbocation rearrangements leading to sativene, cyclosativene, alpha-ylangene, and beta-ylangene. , 2008, The Journal of organic chemistry.

[44]  R. Peters,et al.  Abietadiene synthase catalysis: Mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[45]  D. Tantillo,et al.  Prediction of a new pathway to presilphiperfolanol. , 2008, Organic letters.

[46]  T. Gilbert,et al.  Progressive systematic underestimation of reaction energies by the B3LYP model as the number of C-C bonds increases: why organic chemists should use multiple DFT models for calculations involving polycarbon hydrocarbons. , 2005, The Journal of organic chemistry.

[47]  Donald G Truhlar,et al.  Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions. , 2006, Journal of chemical theory and computation.

[48]  William L. Hase,et al.  Classical trajectory simulations of post-transition state dynamics , 2008 .

[49]  D. Tantillo,et al.  A potential energy surface bifurcation in terpene biosynthesis. , 2009, Nature chemistry.

[50]  Hans Peter Lüthi,et al.  Interaction energies of van der Waals and hydrogen bonded systems calculated using density functional theory: Assessing the PW91 model , 2001 .

[51]  Anthony Goodrow,et al.  Transition state-finding strategies for use with the growing string method. , 2009, The Journal of chemical physics.

[52]  L. Curtiss,et al.  Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation , 1997 .

[53]  M. Harmata,et al.  Control elements in dynamically determined selectivity on a bifurcating surface. , 2008, Journal of the American Chemical Society.

[54]  David E. Bernholdt,et al.  High performance computational chemistry: An overview of NWChem a distributed parallel application , 2000 .

[55]  Donald G Truhlar,et al.  How well can density functional methods describe hydrogen bonds to pi acceptors? , 2005, The journal of physical chemistry. B.

[56]  H. Schaefer,et al.  Problematic Energy Differences between Cumulenes and Poly-ynes: Does This Point to a Systematic Improvement of Density Functional Theory? , 2002 .

[57]  M. Abe,et al.  Notable effect of an electron-withdrawing group at C3 on the selective formation of alkylidenecyclobutanes in the thermal denitrogenation of 4-spirocyclopropane-1-pyrazolines. Nonstatistical dynamics effects in the denitrogenation reactions. , 2007, Journal of the American Chemical Society.

[58]  Lai Xu,et al.  Bifurcations on potential energy surfaces of organic reactions. , 2008, Angewandte Chemie.

[59]  R. Peters,et al.  Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. , 2001, Journal of the American Chemical Society.

[60]  R. Peters,et al.  A single residue switch converts abietadiene synthase into a pimaradiene specific cyclase. , 2007, Journal of the American Chemical Society.

[61]  D. J. Mann,et al.  Ab initio direct dynamics study of cyclopropyl radical ring-opening. , 2002, Journal of the American Chemical Society.

[62]  R. Peters,et al.  Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. , 2000, Biochemistry.

[63]  W. C. Swope,et al.  A computer simulation method for the calculation of equilibrium constants for the formation of physi , 1981 .

[64]  J. P. Chesick The Kinetics of Thermal Isomerization of Methylcyclopropane , 1960 .

[65]  L. Curtiss,et al.  Assessment of Gaussian-3 and density functional theories for a larger experimental test set , 2000 .

[66]  B. L. Kalra,et al.  KINETICS OF THE THERMAL ISOMERIZATION OF METHYLCYCLOPROPANE , 1999 .

[67]  D. Tantillo Recent excursions to the borderlands between the realms of concerted and stepwise: carbocation cascades in natural products biosynthesis , 2008 .

[68]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[69]  M. Frisch,et al.  Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .

[70]  Jun Li,et al.  Basis Set Exchange: A Community Database for Computational Sciences , 2007, J. Chem. Inf. Model..

[71]  D. Christianson,et al.  Structural biology and chemistry of the terpenoid cyclases. , 2006, Chemical reviews.

[72]  W. Hase,et al.  Born–Oppenheimer Direct Dynamics Classical Trajectory Simulations , 2003 .

[73]  G. Dive,et al.  Critical points and reaction paths characterization on a potential energy hypersurface , 2000 .

[74]  Kihyung Song,et al.  A SN2 Reaction That Avoids Its Deep Potential Energy Minimum , 2002, Science.

[75]  Dean J Tantillo,et al.  Which is more likely in trichodiene biosynthesis: hydride or proton transfer? , 2006, Organic letters.

[76]  T. H. Dunning Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[77]  P. Schreiner,et al.  Many density functional theory approaches fail to give reliable large hydrocarbon isomer energy differences. , 2006, Organic letters.

[78]  M. Siebert,et al.  Brother versus brother: competitive stabilization of carbocationic centers by flanking cyclopropanes and π‐systems , 2007 .

[79]  A. Seiter,et al.  High-order symplectic integration: an assessment , 2000 .

[80]  Xiche Hu,et al.  Vectorization of the general Monte Carlo classical trajectory program VENUS , 1991 .

[81]  D. A. Dougherty,et al.  Cation-π Interactions in Chemistry and Biology: A New View of Benzene, Phe, Tyr, and Trp , 1996, Science.

[82]  R. Croteau,et al.  Diterpenoid resin acid biosynthesis in conifers: characterization of two cytochrome P450-dependent monooxygenases and an aldehyde dehydrogenase involved in abietic acid biosynthesis. , 1994, Archives of biochemistry and biophysics.

[83]  Gregory Ho,et al.  Carbocation rearrangements in aspernomine biosynthesis , 2009 .

[84]  D. Tantillo,et al.  Perturbing the structure of the 2-norbornyl cation through C-H...N and C-H...pi interactions. , 2007, Journal of Organic Chemistry.

[85]  A. Seiter,et al.  Symplectic Integration of Classical Trajectories: A Case Study , 1998 .

[86]  Phillips,et al.  Resin-based defenses in conifers. , 1999, Trends in plant science.

[87]  Upakarasamy Lourderaj,et al.  Direct dynamics simulations using Hessian-based predictor-corrector integration algorithms. , 2007, The Journal of chemical physics.