Computational optimization of electric fields for better catalysis design

Although the ubiquitous role that long-ranged electric fields play in catalysis has been recognized, it is seldom used as a primary design parameter in the discovery of new catalytic materials. Here we illustrate how electric fields have been used to computationally optimize biocatalytic performance of a synthetic enzyme, and how they could be used as a unifying descriptor for catalytic design across a range of homogeneous and heterogeneous catalysts. Although focusing on electrostatic environmental effects may open new routes toward the rational optimization of efficient catalysts, much more predictive capacity is required of theoretical methods to have a transformative impact in their computational design — and thus experimental relevance — when using electric field alignments in the reactive centres of complex catalytic systems.The general importance of electrostatic effects on catalysis is well appreciated, but their use in catalyst design is both promising and challenging. This Perspective discusses recent progress and future directions towards computational optimization of biological and chemical catalysis in terms of electric fields and their connections to experimental catalytic systems.

[1]  F. Peeters,et al.  Electric-field-induced structural changes in water confined between two graphene layers , 2016, 1601.06073.

[2]  William L Jorgensen,et al.  Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations. , 2007, Journal of chemical theory and computation.

[3]  J. Dawlaty,et al.  Solvation Reaction Field at the Interface Measured by Vibrational Sum Frequency Generation Spectroscopy. , 2017, Journal of the American Chemical Society.

[4]  H. Freund,et al.  Models in Catalysis , 2014, Catalysis Letters.

[5]  F. Illas,et al.  Electric field effects in heterogeneous catalysis , 1997 .

[6]  J. Kolis,et al.  Diels-Alder reactions using supercritical water as an aqueous solvent medium , 1997 .

[7]  Mark E Tuckerman,et al.  A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps. , 2016, Journal of chemical theory and computation.

[8]  R. Simons,et al.  Strong electric field effects on proton transfer between membrane-bound amines and water , 1979, Nature.

[9]  David M. Kaphan,et al.  Enabling New Modes of Reactivity via Constrictive Binding in a Supramolecular-Assembly-Catalyzed Aza-Prins Cyclization. , 2015, Journal of the American Chemical Society.

[10]  P. Geissler,et al.  Interfacial ion solvation: Obtaining the thermodynamic limit from molecular simulations. , 2018, The Journal of chemical physics.

[11]  Arieh Warshel,et al.  Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases. , 2017, ACS catalysis.

[12]  Ivan V Korendovych,et al.  Catalytic efficiency of designed catalytic proteins. , 2014, Current opinion in structural biology.

[13]  J. Clegg,et al.  Reactivity modulation in container molecules , 2011 .

[14]  M. Head‐Gordon,et al.  Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. , 2017, Journal of chemical theory and computation.

[15]  Arieh Warshel,et al.  Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization , 2010, Proceedings of the National Academy of Sciences.

[16]  Scott Calabrese Barton,et al.  Enzymatic biofuel cells for implantable and micro-scale devices , 2004 .

[17]  R. Pollack Enzymatic mechanisms for catalysis of enolization: ketosteroid isomerase. , 2004, Bioorganic chemistry.

[18]  V. Vitale,et al.  Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory. , 2017, The Journal of chemical physics.

[19]  S. M. Csicsery Shape-selective catalysis in zeolites , 1984 .

[20]  António J. M. Ribeiro,et al.  Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease , 2015 .

[21]  S. Hecht,et al.  Electric field-induced isomerization of azobenzene by STM. , 2006, Journal of the American Chemical Society.

[22]  David Baker,et al.  An exciting but challenging road ahead for computational enzyme design , 2010, Protein science : a publication of the Protein Society.

[23]  J. Nørskov,et al.  Electric Field Effects in Electrochemical CO2 Reduction , 2016 .

[24]  Soumya Ghosh,et al.  Theoretical Insights into Proton-Coupled Electron Transfer from a Photoreduced ZnO Nanocrystal to an Organic Radical. , 2017, Nano letters.

[25]  Soumya Ghosh,et al.  Role of Proton Diffusion in the Nonexponential Kinetics of Proton-Coupled Electron Transfer from Photoreduced ZnO Nanocrystals. , 2017, ACS nano.

[26]  A. Warshel,et al.  Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis , 2017, Proteins.

[27]  Yihan Shao,et al.  TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. , 2016, The Journal of chemical physics.

[28]  David T. Limmer,et al.  Nanoscale heterogeneity at the aqueous electrolyte-electrode interface , 2014, 1410.1239.

[29]  E. Iglesia,et al.  Toward More Complete Descriptors of Reactivity in Catalysis by Solid Acids , 2016 .

[30]  David M. Kaphan,et al.  Scope and Mechanism of Cooperativity at the Intersection of Organometallic and Supramolecular Catalysis. , 2016, Journal of the American Chemical Society.

[31]  Kathleen A. Schwarz,et al.  Evaluating continuum solvation models for the electrode-electrolyte interface: Challenges and strategies for improvement. , 2016, The Journal of chemical physics.

[32]  W. Goddard,et al.  Full atomistic reaction mechanism with kinetics for CO reduction on Cu(100) from ab initio molecular dynamics free-energy calculations at 298 K , 2017, Proceedings of the National Academy of Sciences.

[33]  M. Fuxreiter,et al.  Optimization of reorganization energy drives evolution of the designed Kemp eliminase KE07. , 2013, Biochimica et biophysica acta.

[34]  Kathleen A. Schwarz,et al.  Spicing up continuum solvation models with SaLSA: the spherically averaged liquid susceptibility ansatz. , 2014, The Journal of chemical physics.

[35]  D. Prendergast,et al.  The Formation Time of Ti-O• and Ti-O•-Ti Radicals at the n-SrTiO3/Aqueous Interface during Photocatalytic Water Oxidation. , 2017, Journal of the American Chemical Society.

[36]  Sudhir C. Sharma,et al.  Computational Optimization of Electric Fields for Improving Catalysis of a Designed Kemp Eliminase , 2018 .

[37]  Lisa E. Felberg,et al.  Coexistence of Multilayered Phases of Confined Water: The Importance of Flexible Confining Surfaces. , 2018, ACS nano.

[38]  T. Van Voorhis,et al.  Quantum chemical approaches to [NiFe] hydrogenase. , 2017, Essays in biochemistry.

[39]  V. Lee Heterogeneous Catalysis: Effect of an Alternating Electric Field , 1966, Science.

[40]  M. Head‐Gordon,et al.  Impact of long-range electrostatic and dispersive interactions on theoretical predictions of adsorption and catalysis in zeolites , 2018, Catalysis Today.

[41]  Erkang Wang,et al.  Nanomaterials with Enzyme-Like Characteristics (Nanozymes): Next-Generation Artificial Enzymes , 2013 .

[42]  M. Head‐Gordon,et al.  Mapping the genome of meta-generalized gradient approximation density functionals: the search for B97M-V. , 2015, The Journal of chemical physics.

[43]  D. Herschlag,et al.  Comment on “Extreme electric fields power catalysis in the active site of ketosteroid isomerase” , 2015, Science.

[44]  Francois Gygi,et al.  Strongly Anisotropic Dielectric Relaxation of Water at the Nanoscale , 2013 .

[45]  Alfred B. Anderson,et al.  Electronic structure calculations of liquid-solid interfaces: Combination of density functional theory and modified Poisson-Boltzmann theory , 2008 .

[46]  A. Tokmakoff,et al.  Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. , 2016, Annual review of physical chemistry.

[47]  J. Nørskov,et al.  Unifying Kinetic and Thermodynamic Analysis of 2 e– and 4 e– Reduction of Oxygen on Metal Surfaces , 2014 .

[48]  Thomas E Markland,et al.  Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. , 2017, The journal of physical chemistry. B.

[49]  F. Hirata,et al.  Solvent Effects on a Diels−Alder Reaction in Supercritical Water: RISM-SCF Study , 2000 .

[50]  S. Benkovic,et al.  Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase , 2014, Journal of the American Chemical Society.

[51]  C. Copéret,et al.  Homogeneous and heterogeneous catalysis: bridging the gap through surface organometallic chemistry. , 2003, Angewandte Chemie.

[52]  M. Dusselier,et al.  Shape-selective zeolite catalysis for bioplastics production , 2015, Science.

[53]  Oleksandr Voznyy,et al.  Enhanced electrocatalytic CO2 reduction via field-induced reagent concentration , 2016, Nature.

[54]  D. Marx,et al.  Nanoconfinement in Slit Pores Enhances Water Self-Dissociation. , 2017, Physical review letters.

[55]  M. Head‐Gordon,et al.  Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals , 2017 .

[56]  Chris-Kriton Skylaris,et al.  Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals. , 2017, The journal of physical chemistry letters.

[57]  M. Kanan,et al.  An electric field-induced change in the selectivity of a metal oxide-catalyzed epoxide rearrangement. , 2012, Journal of the American Chemical Society.

[58]  J. Dawlaty,et al.  Direct Spectroscopic Measurement of Interfacial Electric Fields near an Electrode under Polarizing or Current-Carrying Conditions , 2017 .

[59]  Arieh Warshel,et al.  Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase , 2010, Proceedings of the National Academy of Sciences.

[60]  D. Matyushov,et al.  Dielectric constant of water in the interface. , 2016, The Journal of chemical physics.

[61]  Head-Gordon,et al.  On the Use of the rVV 10 Nonlocal Correlation Functional in the B 97 MV Density Functional : Defining B 97 MrV and Related Functionals , 2017 .

[62]  S. Boxer,et al.  Electric Fields and Enzyme Catalysis. , 2017, Annual review of biochemistry.

[63]  Sason Shaik,et al.  Oriented electric fields as future smart reagents in chemistry. , 2016, Nature chemistry.

[64]  Robert Schlögl,et al.  The Haber-Bosch process revisited: on the real structure and stability of "ammonia iron" under working conditions. , 2013, Angewandte Chemie.

[65]  Teresa Head-Gordon,et al.  The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70. , 2016, Physical chemistry chemical physics : PCCP.

[66]  A. Warshel,et al.  Energetics of enzyme catalysis. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[67]  S. Matile,et al.  Electric-Field-Assisted Anion-π Catalysis. , 2017, Journal of the American Chemical Society.

[68]  Gordon G. Wallace,et al.  Electrostatic catalysis of a Diels–Alder reaction , 2016, Nature.

[69]  S. Boxer,et al.  Extreme electric fields power catalysis in the active site of ketosteroid isomerase , 2014, Science.

[70]  Teresa Head-Gordon,et al.  Accurate Classical Polarization Solution with No Self-Consistent Field Iterations. , 2017, The journal of physical chemistry letters.

[71]  Ranko Goic,et al.  review of solar photovoltaic technologies , 2011 .

[72]  Jean-Marie Basset,et al.  Homogeneous and heterogeneous catalysis: bridging the gap through surface organometallic chemistry. , 2003, Angewandte Chemie.

[73]  A. Warshel,et al.  Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase. , 2004, Journal of the American Chemical Society.

[74]  D. Marx,et al.  Bicanonical ab Initio Molecular Dynamics for Open Systems. , 2017, Journal of chemical theory and computation.

[75]  Thomas E. Markland,et al.  Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory. , 2015, The Journal of chemical physics.

[76]  Teresa Head-Gordon,et al.  The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase. , 2017, Journal of the American Chemical Society.

[77]  U. Ryde,et al.  Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods , 2016, JBIC Journal of Biological Inorganic Chemistry.

[78]  A. Warshel,et al.  Electrostatic origin of the catalytic effect of a supramolecular host catalyst. , 2012, The journal of physical chemistry. B.

[79]  Joachim Sauer,et al.  Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy , 2016, Angewandte Chemie.

[80]  Ronald Breslow,et al.  Hydrophobic acceleration of Diels-Alder reactions , 1980 .