Computational Catalysis

276 Pages·2013·9.42 MB·English

by  Aravind Asthagiri

Computational Catalysis
1
0
0
P
F
5-
0
9
4
3
7
9
4
8
1
8
7
9
9/
3
0
1
0.
1
oi:
d
g |
or
c.
s
s.r
b
u
p
p://
htt
n
o
3
1
0
2
er
b
m
e
c
e
D
2
. n 0
o
d
e
h
s
bli
u
P
View Online
RSC Catalysis Series
Series Editor:
Professor James J Spivey, Louisiana State University, Baton Rouge, USA
1
0
0
P
F Advisory Board:
5-
90 Krijn P de Jong, University of Utrecht, The Netherlands, James A Dumesic,
4
73 University of Wisconsin-Madison, USA, Chris Hardacre, Queen’s University
9
84 Belfast, Northern Ireland, Enrique Iglesia, University of California at Berkeley,
1
8 USA, Zinfer Ismagilov, Boreskov Institute of Catalysis, Novosibirsk, Russia,
7
9
9/ JohannesLercher,TUMu¨nchen,Germany,UmitOzkan,OhioStateUniversity,
3
10 USA, Chunshan Song, Penn State University, USA
0.
1
oi:
d Titles in the Series:
g |
or 1: Carbons and Carbon Supported Catalysts in Hydroprocessing
sc. 2: Chiral Sulfur Ligands: Asymmetric Catalysis
s.r
b 3: Recent Developments in Asymmetric Organocatalysis
u
p
p:// 4: Catalysis in the Refining of Fischer–Tropsch Syncrude
htt 5: Organocatalytic Enantioselective Conjugate Addition Reactions:
n
o APowerfulToolfortheStereocontrolledSynthesisofComplexMolecules
3
1 6: N-Heterocyclic Carbenes: From Laboratory Curiosities to Efficient
0
2
er Synthetic Tools
b
m 7: P-Stereogenic Ligands in Enantioselective Catalysis
e
ec 8: Chemistry of the Morita–Baylis–Hillman Reaction
D
2 9: Proton-Coupled Electron Transfer: A Carrefour of Chemical Reactivity
. on 0 Traditions
d
e 10: Asymmetric Domino Reactions
h
s
bli 11: C–H and C–X Bond Functionalization: Transition Metal Mediation
u
P 12: Metal Organic Frameworks as Heterogeneous Catalysts
13: Environmental Catalysis Over Gold-Based Materials
14: Computational Catalysis
How to obtain future titles on publication:
A standing order plan is available for this series. A standing order will bring
delivery of each new volume immediately on publication.
For further information please contact:
BookSalesDepartment,RoyalSocietyofChemistry,ThomasGrahamHouse,
Science Park, Milton Road, Cambridge, CB4 0WF, UK
Telephone: [phone],Fax:[phone]
Email:[email protected]
Visit our website atwww.rsc.org/books
View Online
Computational Catalysis
1
0
0
P
F
5- Edited by
0
9
4
3
7
9 Aravind Asthagiri
4
8
81 Ohio State University, USA
7
9/9 Email: [email protected]
3
0
1
10. and
oi:
d
g |
or Michael J. Janik
c.
s.rs Pennsylvania State University, USA
ub Email: [email protected]
p
p://
htt
n
o
3
1
0
2
er
b
m
e
c
e
D
2
. n 0
o
d
e
h
s
bli
u
P
View Online
1
0
0
P
F
5-
0
9
4
3
7
9
4
8
1
8
7
9
9/
3
0
1
0.
1
oi:
d
g |
or
c.
s
s.r
b
u
p
p://
htt
n
o RSCCatalysisSeriesNo.14
3
1
0
2
er ISBN:978-1-84973-451-6
mb ISSN:1757-6725
e
c
e
D AcataloguerecordforthisbookisavailablefromtheBritishLibrary
2
. on 0 rTheRoyalSocietyofChemistry2014
d
e
h
blis Allrightsreserved
u
P
Apartfromfairdealingforthepurposesofresearchfornon-commercialpurposesorfor
privatestudy,criticismorreview,aspermittedundertheCopyright,DesignsandPatents
Act1988andtheCopyrightandRelatedRightsRegulations2003,thispublicationmaynot
bereproduced,storedortransmitted,inanyformorbyanymeans,withouttheprior
permissioninwritingofTheRoyalSocietyofChemistryorthecopyrightowner,orinthe
caseofreproductioninaccordancewiththetermsoflicencesissuedbytheCopyright
LicensingAgencyintheUK,orinaccordancewiththetermsofthelicencesissuedbythe
appropriateReproductionRightsOrganizationoutsidetheUK.Enquiriesconcerning
reproductionoutsidethetermsstatedhereshouldbesenttoTheRoyalSocietyof
Chemistryattheaddressprintedonthispage.
TheRSCisnotresponsibleforindividualopinionsexpressedinthiswork.
PublishedbyTheRoyalSocietyofChemistry,
ThomasGrahamHouse,SciencePark,MiltonRoad,
CambridgeCB40WF,UK
RegisteredCharityNumber207890
Forfurtherinformationseeourwebsiteatwww.rsc.org
5
0
0
P
F
5-
90 Preface
4
3
7
9
4
8
1
8
7
9
9/
3
0
1
0.
1
oi: The RSC Catalysis Book Series has been publishing books focused on many
d
g | aspectsofcatalysissincethe1970’s,buttodatetherehasnotbeenabookinthe
or series that has solely focused on computational modeling of heterogeneous
c.
s.rs catalysis. The importance of computational catalysis has grown over the past
ub twodecadesandthereareanincreasingnumberofyoungresearchersentering
p
p:// this area. The aim of this book is to provide a pedantic presentation of select
htt methods in computational catalysis. Our hope is that this book will prove
n
3 o useful to the graduate student or other researchers already familiar with
1
0 computer simulations, but interested in applying specific methods to their
2
er catalysis research.
b
m
e In the first chapter, Lars Grabow (University of Houston) discusses the
c
De screeningofcatalyststhroughtheuseoffirst-principlesmethods.Usingdensity
. n 02 functional theory (DFT), key descriptors and scaling relationships can be
o identified and incorporated with an appropriate microkinetic model. Such an
d
he approach allows for the rapid screening of materials based on DFT
s
bli calculations.
u
P
One of the key challenges in modeling catalysts is the need to predict the
appropriate surface structure at reaction conditions. Jason Bray and Bill
Schneider (Notre Dame) present a detailed example of a first-principles based
thermodynamic model for oxygen adsorption on Pt surfaces. They derive a
cluster expansion model, fit to DFT data, which allows for exploring the
complexheterogeneousoxygenphaseasafunctionoftemperatureandoxygen
partialpressureusingMonteCarlosimulations.Thesetypesofsimulationsalso
allow for exploring surface reaction behavior under reaction conditions.
Inthe third chapter,Kuan-YuYeh andMikeJanik (Penn State University)
present a detailed review of DFT-based modeling of electrocatalysts. The
electrochemicalinterfaceisoneofthemorechallengingenvironmentstomodel,
and several different models that vary in accuracy and computational expense
RSCCatalysisSeriesNo.14
ComputationalCatalysis
EditedbyAravindAsthagiriandMichaelJ.Janik
rTheRoyalSocietyofChemistry2014
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
v
View Online
vi Preface
are presented. With these methods potential dependent reaction energies and
barrierscanbecalculatedforelementarysteps.Specificexamplesarepresented
to illustrate how to apply these various models.
Another important area of computational catalysis is modeling the metal/
05 oxide interface, which is discussed by Tom Senftle, Adri van Duin, and Mike
0
FP Janik(PennState).Theyreviewseveralapplications,suchasthewater-gasshift
5-
0 reaction and hydrocarbon activation, and the stability of oxide phases, that
9
4
3 applies both DFT-based calculations and charge transfer potentials.
7
9
4 Thomas Manz (New Mexico State University) and David Sholl (Georgia
8
1
8 Tech) present the details and application of their charge partitioning method
7
9/9 called the density derived electrostatic and chemical (DDEC) method. This
3
0 method can be used to obtain chemically relevant atomic charges and spin
1
10. momentsforbothperiodicandnon-periodicsystems.Suchoutputcanassistin
doi: understanding the relationship between electronic structure and material
g | properties,andcanalsobeusedasinputintothefittingofclassicalpotentials.
or
c. The last two chapters present details of two classical potentials that in-
s
bs.r corporatechargetransfer.AdrivanDuinandco-workerspresentthedetailsof
u
http://p twhoerkReerasxfFrFompottheentUianliavnedrsidtyiscoufssFsloevriedraalparpepselinctattihoensc.hSaursgaenoSpitninmoitztedanmdacnoy-
n body(COMB)potentialsanditsapplicationtomoleculesandmetalsonoxide
o
13 surfaces.
0
er 2 We appreciate the efforts made by the authors to present a wide range of
mb important methods in computational catalysis at a level that can benefit a
e
c researcher learning these methods for their research.
e
D
2
. n 0 Aravind Asthagiri
o
d Michael J Janik
e
h
s
bli
u
P
7
0
0
P
F
5-
90 Contents
4
3
7
9
4
8
1
8
7
9
9/
3
10 Chapter 1 Computational Catalyst Screening 1
0.
1 Lars C. Grabow
oi:
d
org | 1.1 Introduction 1
sc. 1.1.1 A Walk through a Computational Catalyst
bs.r Design Process: Methanation 3
u
p
p:// 1.2 Starting from the Electronic Structure 4
htt 1.2.1 Density Functional Theory 4
on 1.2.2 The d-Band Model 6
3
1 1.3 Identifying the Right Descriptor Set 8
0
2
er 1.3.1 Scaling Relations for Surface
b
m Intermediates 9
e
ec 1.3.2 Scaling Relations for Transition States:
D
2 The Brønsted–Evans–Polanyi
. n 0 Relationship 13
o
ed 1.4 The Sabatier Principle and the Volcano Curve 17
h
s
bli 1.4.1 Sabatier Analysis 18
u
P 1.5 Sabatier Analysis in Practice 20
1.5.1 First Example: Ammonia Synthesis 20
1.5.2 Second Example: CO Oxidation 25
1.6 Notes on Microkinetic Modeling 27
1.6.1 Numerical Solution Strategies 29
1.6.2 Entropy and Enthalpy Corrections 31
1.6.3 Microkinetic Model Analysis 32
1.7 CO Oxidation Catalyst Screening 35
1.7.1 Numerical Microkinetic Model 35
1.7.2 Degree of Rate and Catalyst Control 41
1.7.3 Two-dimensional CO Oxidation Volcano 44
1.7.4 Effect of Lateral Interactions 45
RSCCatalysisSeriesNo.14
ComputationalCatalysis
EditedbyAravindAsthagiriandMichaelJ.Janik
rTheRoyalSocietyofChemistry2014
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
vii
View Online
viii Contents
1.8 Conclusions 47
Appendix 48
References 55
7
0
0 Chapter 2 First-principles Thermodynamic Models in Heterogeneous
P
F
5- Catalysis 59
0
49 J. M. Bray and W. F. Schneider
3
7
9
4
18 2.1 Introduction 59
8
7 2.1.1 Background 59
9
39/ 2.1.2 Background on Oxygen Adsorption on
0
0.1 Platinum 62
1
oi: 2.2 Setting up the System 63
d
g | 2.2.1 Developing a Slab Model 63
or 2.2.2 Identifying and Characterizing Adsorption
c.
s.rs Sites 65
b
u 2.2.3 Increasing Coverage 69
p
p:// 2.3 DevelopingaSelf-consistentClusterExpansionModel 72
htt 2.3.1 Cluster Expansion Fundamentals 72
n
3 o 2.3.2 Self-consistent Fitting Approach 74
1
0 2.4 Applying the Model to Obtain Physical Insight 80
2
er 2.4.1 Analysis of the DFT Fitting Database 80
b
m
e 2.4.2 Analysis of Ordered Ground States 83
c
De 2.4.3 Monte Carlo Simulations 93
. n 02 2.4.4 Kinetic Properties from CE/GCMC Methods 109
o 2.5 Conclusions 112
d
he Acknowledgments 112
s
bli References 113
u
P
Chapter 3 Density Functional Theory Methods for Electrocatalysis 116
Kuan-Yu Yeh and Michael J. Janik
3.1 Introduction 116
3.1.1 A Motivating Example: H Oxidation/H
2 2
Evolution 117
3.1.2 Electrode Potential Effects on Reaction
Energies and Activation Barriers 121
3.1.3 Electrochemical Double-layer Theory 122
3.1.4 Overview of DFT Models for Electrocatalysis 124
3.2 Examples Applying DFT Methods to
Electrocatalysis 128
3.2.1 Simulating the Vacuum–Metal Interface 129
3.2.2 Simulating an Aqueous–Metal Interface 137
3.2.3 Linear Sweep Voltammetry Simulations 146
View Online
Contents ix
3.2.4 Calculation of Surface Reaction Free
Energies 147
3.2.5 Potential Dependent Activation Barriers 151
3.3 Conclusions 153
07 References 153
0
P
F
5-
0
9 Chapter 4 Application of Computational Methods to Supported
4
3
7 Metal–Oxide Catalysis 157
9
4
8 ThomasP.Senftle,AdriC.T.vanDuinandMichaelJ.Janik
1
8
7
9
39/ 4.1 Introduction 157
0
0.1 4.2 Computational Approaches to Supported
1
oi: Metal–Oxide Catalysis 158
d
g | 4.3 Selected Applications 159
or 4.3.1 Application of DFT to WGS 161
c.
s.rs 4.3.2 Ab Initio Thermodynamics 167
b
u 4.3.3 Classical Atomistic Modeling 174
p
p:// 4.3.4 Combined Application: Hydrocarbon
htt Activation over Pd/CeO 178
n 2
3 o 4.4 Conclusions 185
1
0 References 186
2
er
b
m
ce Chapter 5 Computing Accurate Net Atomic Charges, Atomic Spin
e
D
2 Moments, and Effective Bond Orders in Complex
. n 0 Materials 192
o
d Thomas A. Manz and David S. Sholl
e
h
s
bli
u 5.1 Introduction 192
P
5.2 Net Atomic Charges and Atomic Spin Moments 194
5.2.1 The Charge Partitioning Functional 194
5.2.2 The Spin Partitioning Functional 196
5.2.3 Example using VASP Software 198
5.2.4 Examples using GAUSSIAN Software 201
5.2.5 VASP Non-collinear Magnetism Example 205
5.3 Modeling the Electrostatic Potential Surrounding a
Material 209
5.3.1 Atom-centered Distributed Multipole
Expansion 209
5.3.2 Applications to Force-fields used in Atomistic
Simulations 211
5.4 Effective Bond Orders 212
5.5 Conclusions 219
Acknowledgments 219
References 220
View Online
x Contents
Chapter6 AReaxffReactiveForce-fieldforProtonTransferReactions
in Bulk Water and its Applications to Heterogeneous
Catalysis 223
Adri C.T. van Duin, Chenyu Zou, Kaushik Joshi,
7
0 Vyascheslav Bryantsev and William A. Goddard
0
P
F
5-
0 6.1 Introduction 223
9
4
3 6.2 Methods 226
7
9
4 6.2.1 Quantumchemical Methods 226
8
1
8 6.2.2 Force-field Optimization 226
7
9
9/ 6.3 Results and Discussion 226
3
10 6.3.1 Force-field Development 226
0.
1 6.3.2 Molecular Dynamics Simulations 233
oi:
d 6.3.3 Heterogeneous Catalysis 238
org | 6.4 Conclusions 240
sc. References 240
s.r
b
u
p://p Chapter 7 Charge Transfer Potentials 244
htt Yu-Ting Cheng, Tao Liang, Simon R. Phillpot and
on Susan B. Sinnott
3
1
0
2
er 7.1 Introduction 244
b
m 7.2 Variable Charge Reactive Potentials: COMB
e
c
e Potentials 247
D
2 7.2.1 A General Form of the COMB Potentials 247
. on 0 7.2.2 Electrostatic Energies 247
d
he 7.2.3 Short-range Interactions 249
s
bli 7.2.4 van der Waals Interactions 251
u
P 7.2.5 Correction Terms 251
7.2.6 Parameterization of the COMB Potential 251
7.3 Applications 255
7.3.1 Ethyl Radical Deposition on the Cu(111)
Surface 255
7.3.2 Cu/ZnO Heterogeneous System 256
7.4 Conclusions 257
Acknowledgments 258
References 258
Subject Index 261