skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Computational optimization of electric fields for better catalysis design

Abstract

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 in this paper, 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.

Authors:
 [1];  [1]; ORCiD logo [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Chemical Sciences Division; Pitzer Center for Theoretical Chemistry, Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Chemical Sciences Division, Dept. of Chemistry, Chemical and Biomolecular Engineering, Bioengineering; Pitzer Center for Theoretical Chemistry, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Chemical Sciences, Geosciences & Biosciences Division; USDOE Office of Science (SC)
OSTI Identifier:
1487215
Alternate Identifier(s):
OSTI ID: 1506348
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Catalysis
Additional Journal Information:
Journal Volume: 1; Journal Issue: 9; Journal ID: ISSN 2520-1158
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 97 MATHEMATICS AND COMPUTING

Citation Formats

Welborn, Valerie Vaissier, Ruiz Pestana, Luis, and Head-Gordon, Teresa. Computational optimization of electric fields for better catalysis design. United States: N. p., 2018. Web. doi:10.1038/s41929-018-0109-2.
Welborn, Valerie Vaissier, Ruiz Pestana, Luis, & Head-Gordon, Teresa. Computational optimization of electric fields for better catalysis design. United States. doi:10.1038/s41929-018-0109-2.
Welborn, Valerie Vaissier, Ruiz Pestana, Luis, and Head-Gordon, Teresa. Mon . "Computational optimization of electric fields for better catalysis design". United States. doi:10.1038/s41929-018-0109-2. https://www.osti.gov/servlets/purl/1487215.
@article{osti_1487215,
title = {Computational optimization of electric fields for better catalysis design},
author = {Welborn, Valerie Vaissier and Ruiz Pestana, Luis and Head-Gordon, Teresa},
abstractNote = {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 in this paper, 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.},
doi = {10.1038/s41929-018-0109-2},
journal = {Nature Catalysis},
number = 9,
volume = 1,
place = {United States},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 22 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease
journal, August 2015

  • Ribeiro, António J. M.; Santos-Martins, Diogo; Russo, Nino
  • ACS Catalysis, Vol. 5, Issue 9
  • DOI: 10.1021/acscatal.5b00759

Enzymatic Biofuel Cells for Implantable and Microscale Devices
journal, October 2004

  • Calabrese Barton, Scott; Gallaway, Josh; Atanassov, Plamen
  • Chemical Reviews, Vol. 104, Issue 10
  • DOI: 10.1021/cr020719k

Enabling New Modes of Reactivity via Constrictive Binding in a Supramolecular-Assembly-Catalyzed Aza-Prins Cyclization
journal, July 2015

  • Kaphan, David M.; Toste, F. Dean; Bergman, Robert G.
  • Journal of the American Chemical Society, Vol. 137, Issue 29
  • DOI: 10.1021/jacs.5b01261

Nanoconfinement in Slit Pores Enhances Water Self-Dissociation
journal, July 2017


Electric Fields and Enzyme Catalysis
journal, June 2017


Ab Initio Calculation of Rate Constants for Molecule-Surface Reactions with Chemical Accuracy
journal, March 2016

  • Piccini, GiovanniMaria; Alessio, Maristella; Sauer, Joachim
  • Angewandte Chemie International Edition, Vol. 55, Issue 17
  • DOI: 10.1002/anie.201601534

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
journal, September 2010

  • Frushicheva, M. P.; Cao, J.; Chu, Z. T.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 39
  • DOI: 10.1073/pnas.1010381107

Theoretical Insights into Proton-Coupled Electron Transfer from a Photoreduced ZnO Nanocrystal to an Organic Radical
journal, August 2017


Optimization of reorganization energy drives evolution of the designed Kemp eliminase KE07
journal, May 2013

  • Labas, A.; Szabo, E.; Mones, L.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 5
  • DOI: 10.1016/j.bbapap.2013.01.005

Dielectric constant of water in the interface
journal, July 2016

  • Dinpajooh, Mohammadhasan; Matyushov, Dmitry V.
  • The Journal of Chemical Physics, Vol. 145, Issue 1
  • DOI: 10.1063/1.4955203

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization
journal, February 2010

  • Kamerlin, S. C. L.; Sharma, P. K.; Chu, Z. T.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 9
  • DOI: 10.1073/pnas.0914579107

Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods
journal, March 2016


Role of Proton Diffusion in the Nonexponential Kinetics of Proton-Coupled Electron Transfer from Photoreduced ZnO Nanocrystals
journal, September 2017

  • Ghosh, Soumya; Soudackov, Alexander V.; Hammes-Schiffer, Sharon
  • ACS Nano, Vol. 11, Issue 10
  • DOI: 10.1021/acsnano.7b05009

Heterogeneous Catalysis: Effect of an Alternating Electric Field
journal, April 1966


An Electric Field–Induced Change in the Selectivity of a Metal Oxide–Catalyzed Epoxide Rearrangement
journal, December 2011

  • Gorin, Craig F.; Beh, Eugene S.; Kanan, Matthew W.
  • Journal of the American Chemical Society, Vol. 134, Issue 1
  • DOI: 10.1021/ja210365j

Diels-Alder reactions using supercritical water as an aqueous solvent medium
journal, August 1997


Shape-selective catalysis in zeolites
journal, July 1984


The Formation Time of Ti–O and Ti–O –Ti Radicals at the n-SrTiO 3 /Aqueous Interface during Photocatalytic Water Oxidation
journal, December 2016

  • Chen, Xihan; Choing, Stephanie N.; Aschaffenburg, Daniel J.
  • Journal of the American Chemical Society, Vol. 139, Issue 5
  • DOI: 10.1021/jacs.6b09550

Electric Field-Induced Isomerization of Azobenzene by STM
journal, November 2006

  • Alemani, Micol; Peters, Maike V.; Hecht, Stefan
  • Journal of the American Chemical Society, Vol. 128, Issue 45, p. 14446-14447
  • DOI: 10.1021/ja065449s

Impact of long-range electrostatic and dispersive interactions on theoretical predictions of adsorption and catalysis in zeolites
journal, August 2018


Full atomistic reaction mechanism with kinetics for CO reduction on Cu(100) from ab initio molecular dynamics free-energy calculations at 298 K
journal, February 2017

  • Cheng, Tao; Xiao, Hai; Goddard, William A.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 8
  • DOI: 10.1073/pnas.1612106114

Nanomaterials with enzyme-like characteristics (nanozymes): next-generation artificial enzymes
journal, January 2013

  • Wei, Hui; Wang, Erkang
  • Chemical Society Reviews, Vol. 42, Issue 14
  • DOI: 10.1039/c3cs35486e

Electrostatic Origin of the Catalytic Effect of a Supramolecular Host Catalyst
journal, November 2012

  • Frushicheva, Maria P.; Mukherjee, Shayantani; Warshel, Arieh
  • The Journal of Physical Chemistry B, Vol. 116, Issue 45
  • DOI: 10.1021/jp3084327

Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases
journal, April 2017


Hydrophobic acceleration of Diels-Alder reactions
journal, December 1980

  • Rideout, Darryl C.; Breslow, Ronald
  • Journal of the American Chemical Society, Vol. 102, Issue 26
  • DOI: 10.1021/ja00546a048

Accurate Classical Polarization Solution with No Self-Consistent Field Iterations
journal, April 2017

  • Albaugh, Alex; Niklasson, Anders M. N.; Head-Gordon, Teresa
  • The Journal of Physical Chemistry Letters, Vol. 8, Issue 8
  • DOI: 10.1021/acs.jpclett.7b00450

Evaluating continuum solvation models for the electrode-electrolyte interface: Challenges and strategies for improvement
journal, February 2017

  • Sundararaman, Ravishankar; Schwarz, Kathleen
  • The Journal of Chemical Physics, Vol. 146, Issue 8
  • DOI: 10.1063/1.4976971

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
journal, September 2016

  • Dziedzic, Jacek; Mao, Yuezhi; Shao, Yihan
  • The Journal of Chemical Physics, Vol. 145, Issue 12
  • DOI: 10.1063/1.4962909

Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals
journal, December 2016

  • Mardirossian, Narbe; Ruiz Pestana, Luis; Womack, James C.
  • The Journal of Physical Chemistry Letters, Vol. 8, Issue 1
  • DOI: 10.1021/acs.jpclett.6b02527

Catalytic efficiency of designed catalytic proteins
journal, August 2014


Homogeneous and Heterogeneous Catalysis: Bridging the Gap through Surface Organometallic Chemistry
journal, January 2003

  • Copéret, Christophe; Chabanas, Mathieu; Petroff Saint-Arroman, Romain
  • Angewandte Chemie International Edition, Vol. 42, Issue 2, p. 156-181
  • DOI: 10.1002/anie.200390072

Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase
journal, July 2014

  • Liu, C. Tony; Layfield, Joshua P.; Stewart, Robert J.
  • Journal of the American Chemical Society, Vol. 136, Issue 29
  • DOI: 10.1021/ja5038947

Oriented electric fields as future smart reagents in chemistry
journal, November 2016

  • Shaik, Sason; Mandal, Debasish; Ramanan, Rajeev
  • Nature Chemistry, Vol. 8, Issue 12
  • DOI: 10.1038/nchem.2651

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
journal, March 2017

  • Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex
  • The Journal of Chemical Physics, Vol. 146, Issue 12
  • DOI: 10.1063/1.4978684

Unifying Kinetic and Thermodynamic Analysis of 2 e and 4 e Reduction of Oxygen on Metal Surfaces
journal, March 2014

  • Hansen, Heine A.; Viswanathan, Venkatasubramanian; Nørskov, Jens K.
  • The Journal of Physical Chemistry C, Vol. 118, Issue 13
  • DOI: 10.1021/jp4100608

Scope and Mechanism of Cooperativity at the Intersection of Organometallic and Supramolecular Catalysis
journal, July 2016

  • Levin, Mark D.; Kaphan, David M.; Hong, Cynthia M.
  • Journal of the American Chemical Society, Vol. 138, Issue 30
  • DOI: 10.1021/jacs.6b05442

Electric-field-induced structural changes in water confined between two graphene layers
journal, July 2016


Energetics of enzyme catalysis.
journal, November 1978


Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
journal, April 2017

  • Mao, Yuezhi; Shao, Yihan; Dziedzic, Jacek
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 5
  • DOI: 10.1021/acs.jctc.7b00089

Computational Optimization of Electric Fields for Improving Catalysis of a Designed Kemp Eliminase
journal, December 2017


Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals
journal, April 2017


Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase"
journal, August 2015


Elucidation of Rate Variations for a Diels−Alder Reaction in Ionic Liquids from QM/MM Simulations
journal, November 2006

  • Acevedo, Orlando; Jorgensen, William L.; Evanseck, Jeffrey D.
  • Journal of Chemical Theory and Computation, Vol. 3, Issue 1
  • DOI: 10.1021/ct6002753

Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase"
journal, August 2015


An exciting but challenging road ahead for computational enzyme design: Computational Enzyme Design
journal, September 2010


The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70
journal, January 2016

  • Bhowmick, Asmit; Sharma, Sudhir C.; Honma, Hallie
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 28
  • DOI: 10.1039/C6CP03622H

Electric Field Effects in Electrochemical CO 2 Reduction
journal, September 2016


Solvation Reaction Field at the Interface Measured by Vibrational Sum Frequency Generation Spectroscopy
journal, February 2017

  • Sorenson, Shayne A.; Patrow, Joel G.; Dawlaty, Jahan M.
  • Journal of the American Chemical Society, Vol. 139, Issue 6
  • DOI: 10.1021/jacs.6b11940

A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps
journal, April 2016

  • Margul, Daniel T.; Tuckerman, Mark E.
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 5
  • DOI: 10.1021/acs.jctc.6b00188

Quantum chemical approaches to [NiFe] hydrogenase
journal, May 2017

  • Vaissier, Valerie; Van Voorhis, Troy
  • Essays in Biochemistry, Vol. 61, Issue 2
  • DOI: 10.1042/EBC20160079

Nanoscale heterogeneity at the aqueous electrolyte–electrode interface
journal, January 2015


Enzymatic mechanisms for catalysis of enolization: ketosteroid isomerase
journal, October 2004


Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis
journal, September 2017

  • Jindal, Garima; Warshel, Arieh
  • Proteins: Structure, Function, and Bioinformatics, Vol. 85, Issue 12
  • DOI: 10.1002/prot.25381

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V
journal, February 2015

  • Mardirossian, Narbe; Head-Gordon, Martin
  • The Journal of Chemical Physics, Vol. 142, Issue 7
  • DOI: 10.1063/1.4907719

Enhanced electrocatalytic CO2 reduction via field-induced reagent concentration
journal, August 2016


Spicing up continuum solvation models with SaLSA: The spherically averaged liquid susceptibility ansatz
journal, February 2015

  • Sundararaman, Ravishankar; Schwarz, Kathleen A.; Letchworth-Weaver, Kendra
  • The Journal of Chemical Physics, Vol. 142, Issue 5
  • DOI: 10.1063/1.4906828

Direct Spectroscopic Measurement of Interfacial Electric Fields near an Electrode under Polarizing or Current-Carrying Conditions
journal, May 2017

  • Patrow, Joel G.; Sorenson, Shayne A.; Dawlaty, Jahan M.
  • The Journal of Physical Chemistry C, Vol. 121, Issue 21
  • DOI: 10.1021/acs.jpcc.7b03134

Strong electric field effects on proton transfer between membrane-bound amines and water
journal, August 1979


Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory
journal, February 2016

  • Marsalek, Ondrej; Markland, Thomas E.
  • The Journal of Chemical Physics, Vol. 144, Issue 5
  • DOI: 10.1063/1.4941093

Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site
journal, October 2017

  • Wang, Lu; Fried, Stephen D.; Markland, Thomas E.
  • The Journal of Physical Chemistry B, Vol. 121, Issue 42
  • DOI: 10.1021/acs.jpcb.7b06985

A review of solar photovoltaic technologies
journal, April 2011

  • Parida, Bhubaneswari; Iniyan, S.; Goic, Ranko
  • Renewable and Sustainable Energy Reviews, Vol. 15, Issue 3
  • DOI: 10.1016/j.rser.2010.11.032

Electric-Field-Assisted Anion−π Catalysis
journal, May 2017

  • Akamatsu, Masaaki; Sakai, Naomi; Matile, Stefan
  • Journal of the American Chemical Society, Vol. 139, Issue 19
  • DOI: 10.1021/jacs.7b02421

Toward More Complete Descriptors of Reactivity in Catalysis by Solid Acids
journal, July 2016


Reactivity modulation in container molecules
journal, January 2011

  • Breiner, Boris; Clegg, Jack K.; Nitschke, Jonathan R.
  • Chem. Sci., Vol. 2, Issue 1
  • DOI: 10.1039/C0SC00329H

Shape-selective zeolite catalysis for bioplastics production
journal, July 2015

  • Dusselier, Michiel; Van Wouwe, Pieter; Dewaele, Annelies
  • Science, Vol. 349, Issue 6243
  • DOI: 10.1126/science.aaa7169

Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Atom Transfer in Lipoxygenase
journal, March 2004

  • Olsson, Mats H. M.; Siegbahn, Per E. M.; Warshel, Arieh
  • Journal of the American Chemical Society, Vol. 126, Issue 9
  • DOI: 10.1021/ja037233l

The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase
journal, April 2017

  • Bhowmick, Asmit; Sharma, Sudhir C.; Head-Gordon, Teresa
  • Journal of the American Chemical Society, Vol. 139, Issue 16
  • DOI: 10.1021/jacs.6b12265

Extreme electric fields power catalysis in the active site of ketosteroid isomerase
journal, December 2014


Solvent Effects on a Diels−Alder Reaction in Supercritical Water:  RISM-SCF Study
journal, March 2000

  • Harano, Yuichi; Sato, Hirofumi; Hirata, Fumio
  • Journal of the American Chemical Society, Vol. 122, Issue 10
  • DOI: 10.1021/ja991673o

Electrostatic catalysis of a Diels–Alder reaction
journal, March 2016

  • Aragonès, Albert C.; Haworth, Naomi L.; Darwish, Nadim
  • Nature, Vol. 531, Issue 7592
  • DOI: 10.1038/nature16989

Coexistence of Multilayered Phases of Confined Water: The Importance of Flexible Confining Surfaces
journal, January 2018

  • Ruiz Pestana, Luis; Felberg, Lisa E.; Head-Gordon, Teresa
  • ACS Nano, Vol. 12, Issue 1
  • DOI: 10.1021/acsnano.7b06805

Strongly Anisotropic Dielectric Relaxation of Water at the Nanoscale
journal, July 2013

  • Zhang, Cui; Gygi, François; Galli, Giulia
  • The Journal of Physical Chemistry Letters, Vol. 4, Issue 15
  • DOI: 10.1021/jz401108n

Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics
journal, May 2016


Models in Catalysis
journal, October 2014


The Haber-Bosch Process Revisited: On the Real Structure and Stability of “Ammonia Iron” under Working Conditions
journal, October 2013

  • Kandemir, Timur; Schuster, Manfred E.; Senyshyn, Anatoliy
  • Angewandte Chemie International Edition, Vol. 52, Issue 48
  • DOI: 10.1002/anie.201305812

Bicanonical ab Initio Molecular Dynamics for Open Systems
journal, July 2017

  • Frenzel, Johannes; Meyer, Bernd; Marx, Dominik
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 8
  • DOI: 10.1021/acs.jctc.7b00263

Electric field effects in heterogeneous catalysis
journal, May 1997

  • Pacchioni, Gianfranco; Lomas, Julian R.; Illas, Francesc
  • Journal of Molecular Catalysis A: Chemical, Vol. 119, Issue 1-3
  • DOI: 10.1016/S1381-1169(96)00490-6