Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part I: Fingerprint Spectra

Aarva, Anja; Deringer, Volker L.; Sainio, Sami; Laurila, Tomi; Caro, Miguel A.

doi:10.1021/acs.chemmater.9b02049

Title: Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part I: Fingerprint Spectra

Authors:

^[1];

^[2];

^[3];

^[1];

^[4]

Department of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, 02150 Espoo, Finland
Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
Department of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, 02150 Espoo, Finland; Department of Applied Physics, Aalto University, 02150 Espoo, Finland

Publication Date:: Mon Oct 28 00:00:00 EDT 2019

Research Org.:: Aalto Univ., Otaniemi (Finland); SLAC National Accelerator Lab., Menlo Park, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1575821

Alternate Identifier(s):: OSTI ID: 1575919; OSTI ID: 1596276

Grant/Contract Number:: AC02-76SF00515; 310574; 285526; 730897

Resource Type:: Published Article

Journal Name:: Chemistry of Materials

Additional Journal Information:: Journal Name: Chemistry of Materials Journal Volume: 31 Journal Issue: 22; Journal ID: ISSN 0897-4756

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats


                    Aarva, Anja, Deringer, Volker L., Sainio, Sami, Laurila, Tomi, and Caro, Miguel A. Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part I: Fingerprint Spectra.  United States: N. p., 2019. 
Web.  doi:10.1021/acs.chemmater.9b02049.

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                    Aarva, Anja, Deringer, Volker L., Sainio, Sami, Laurila, Tomi, & Caro, Miguel A. Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part I: Fingerprint Spectra.  United States.  https://doi.org/10.1021/acs.chemmater.9b02049

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                    Aarva, Anja, Deringer, Volker L., Sainio, Sami, Laurila, Tomi, and Caro, Miguel A. Mon .  
"Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part I: Fingerprint Spectra".  United States.  https://doi.org/10.1021/acs.chemmater.9b02049.

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@article{osti_1575821,

  title        = {Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part I: Fingerprint Spectra},

  author       = {Aarva, Anja and Deringer, Volker L. and Sainio, Sami and Laurila, Tomi and Caro, Miguel A.},

  abstractNote = {},

  doi          = {10.1021/acs.chemmater.9b02049},

  journal      = {Chemistry of Materials},

  number       = 22,

  volume       = 31,

  place        = {United States},

  year         = {Mon Oct 28 00:00:00 EDT 2019},

  month        = {Mon Oct 28 00:00:00 EDT 2019}

}

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Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part II: Quantitative Fitting of Spectra
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https://doi.org/10.1021/jacs.6b01750

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Elucidating the Nature of Pseudo Jahn and #8722;Teller Distortions in LixMnPO4: Combining Density Functional Theory with Soft and Hard X and #8209;ray Spectroscopy

Journal Article Piper L. F. ; Nam, K. ; Quackenbush, N. F. ; ... - The Journal of Physical Chemistry C
https://doi.org/10.1021/jp3122374

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Title: Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part I: Fingerprint Spectra

Citation Formats

Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part II: Quantitative Fitting of Spectra journal, October 2019

Generalized Gradient Approximation Made Simple journal, October 1996

Accurate absolute core-electron binding energies of molecules, solids, and surfaces from first-principles calculations journal, October 2019

First Experimental Evidence of a C-1 s Core Exciton in Amorphous Carbon Films journal, August 1995

Correlation between sp 3 -to-sp 2 Ratio and Surface Oxygen Functionalities in Tetrahedral Amorphous Carbon (ta-C) Thin Film Electrodes and Implications of Their Electrochemical Properties journal, April 2016

A Chemical View on X-ray Photoelectron Spectroscopy: the ESCA Molecule and Surface-to-Bulk XPS Shifts journal, December 2017

Structure of water adsorbed on the open Cu(110) surface: H-up, H-down, or both? journal, October 2006

Connecting Dopant Bond Type with Electronic Structure in N-Doped Graphene journal, July 2012

Spectroscopic observation of oxygen dissociation on nitrogen-doped graphene journal, August 2017

Chemical bonding on surfaces probed by X-ray emission spectroscopy and density functional theory journal, October 2004

An implementation of core level spectroscopies in a real space Projector Augmented Wave density functional theory code journal, November 2011

Atomate: A high-level interface to generate, execute, and analyze computational materials science workflows journal, November 2017

Hybrid carbon based nanomaterials for electrochemical detection of biomolecules journal, July 2017

Electron transport determines the electrochemical properties of tetrahedral amorphous carbon (ta-C) thin films journal, January 2017

On representing chemical environments journal, May 2013

Amorphous carbon as a bio-mechanical coating — mechanical properties and biological applications journal, February 2001

Periodic boundary conditions in ab initio calculations journal, February 1995

Enhanced secondary electron yield from oxidized regions on amorphous carbon films studied by x-ray spectromicroscopy journal, September 1999

Ab Initio Theory of Dynamical Core-Hole Screening in Graphite from X-Ray Absorption Spectra journal, April 2005

Physisorption-Induced C-H Bond Elongation in Methane journal, April 2006

Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method journal, June 2010

XPS O 1s binding energies for polymers containing hydroxyl, ether, ketone and ester groups journal, May 1991

Initial Fe 3 O 4 (100) Formation on Fe(100) journal, May 2019

Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data journal, February 2009

Integrated Carbon Nanostructures for Detection of Neurotransmitters journal, June 2015

Initial Stages of Oxidation on Graphitic Surfaces: Photoemission Study and Density Functional Theory Calculations journal, April 2009

Dynamical effects in x-ray absorption spectra of graphene and monolayered h -BN on Ni(111) journal, February 2010

Offset-corrected Δ -Kohn-Sham scheme for semiempirical prediction of absolute x-ray photoelectron energies in molecules and solids journal, July 2016

Electrochemical reactions of catechol, methylcatechol and dopamine at tetrahedral amorphous carbon (ta-C) thin film electrodes journal, October 2015

A near edge X-ray absorption fine structure study of oxidized single crystal and polycrystalline diamond surfaces journal, May 2014

Role of surface-electrical properties on the cell-viability of carbon thin films grown in nanodomain morphology journal, May 2016

Reconstruction of the diamond (111) surface journal, November 1992

X-ray absorption spectroscopy study of different solid carbon modifications journal, July 1997

Observation of a C- 1 s Core Exciton in Diamond journal, April 1985

Comparing molecules and solids across structural and alchemical space journal, January 2016

On the Nature of Oxygen-Containing Surface Groups on Carbon Nanofibers and Their Role for Platinum Deposition—An XPS and Titration Study journal, May 2009

Quantum confinement-induced tunable exciton states in graphene oxide journal, July 2013

Structural Defects in Graphene journal, November 2010

Automated generation and ensemble-learned matching of X-ray absorption spectra journal, March 2018

Characterization and Electrochemical Properties of Oxygenated Amorphous Carbon (a-C) Films journal, December 2016

A NEXAFS characterization of ion-beam-assisted carbon-sputtered thin films journal, April 1995

Reactivity of Amorphous Carbon Surfaces: Rationalizing the Role of Structural Motifs in Functionalization Using Machine Learning journal, September 2018

Electronic structure of graphite oxide and thermally reduced graphite oxide journal, April 2011

Core level binding energies of functionalized and defective graphene journal, January 2014

Intrinsic core level photoemission of suspended monolayer graphene journal, July 2018

On the origin of core-level binding energy shifts journal, December 1995

Special points for Brillouin-zone integrations journal, June 1976

Multi-walled carbon nanotubes (MWCNTs) grown directly on tetrahedral amorphous carbon (ta-C): An interfacial study journal, June 2015

Doping as a means to probe the potential dependence of dopamine adsorption on carbon-based surfaces: A first-principles study journal, June 2017

Orientation of graphitic planes during the bias-enhanced nucleation of diamond on silicon: An x-ray absorption near-edge study journal, November 1998

Calculation of the graphene C 1 s core level binding energy journal, February 2015

Functional dependence of core-excitation energies journal, December 2004

Calculations of near-edge x-ray-absorption spectra of gas-phase and chemisorbed molecules by means of density-functional and transition-potential theory journal, September 1998

X-ray photoelectron spectroscopy: Progress and perspectives journal, May 2010

Total Electron Yield Soft X-ray Absorption Spectroscopy in the C K Region of the Mixtures of Graphitic Carbons and Diamond for Quantitative Analysis of the sp 2 /sp 3 -Hybridized Carbon Ratio journal, June 2009

Efficient simulation of near-edge x-ray absorption fine structure (NEXAFS) in density-functional theory: Comparison of core-level constraining approaches journal, February 2019

Diamond-like amorphous carbon journal, May 2002

Tunable Magnetism in Carbon‐Ion‐Implanted Highly Oriented Pyrolytic Graphite journal, December 2008

XPS determination of oxygen-containing functional groups on carbon-fibre surfaces and the cleaning of these surfaces journal, October 1990

X-ray absorption spectroscopy (XAS) study of dip deposited a-C:H(OH) thin films journal, August 2004

Overoxidation of carbon-fiber microelectrodes enhances dopamine adsorption and increases sensitivity journal, January 2003

Carbon nanotube (CNT) forest grown on diamond-like carbon (DLC) thin films significantly improves electrochemical sensitivity and selectivity towards dopamine journal, May 2015

High-throughput computational X-ray absorption spectroscopy journal, July 2018

Thermal Stability and Reducibility of Oxygen-Containing Functional Groups on Multiwalled Carbon Nanotube Surfaces: A Quantitative High-Resolution XPS and TPD/TPR Study journal, October 2008

Ab initio molecular simulations with numeric atom-centered orbitals journal, November 2009

The effect of hydrogen on the electronic and bonding properties of amorphous carbon journal, November 2006

The Structure of Graphite Oxide: Investigation of Its Surface Chemical Groups journal, May 2010

Absolute Binding Energies of Core Levels in Solids from First Principles journal, January 2017

Core-Level Binding Energies from GW : An Efficient Full-Frequency Approach within a Localized Basis journal, August 2018

Atomic and electronic structure of tetrahedral amorphous carbon surfaces from density functional theory: Properties and simulation strategies journal, October 2014

Computational Surface Chemistry of Tetrahedral Amorphous Carbon by Combining Machine Learning and Density Functional Theory journal, September 2018

X-ray absorption near-edge structure calculations with the pseudopotentials: Application to the K edge in diamond and α -quartz journal, November 2002

Optimizing many-body atomic descriptors for enhanced computational performance of machine learning based interatomic potentials journal, July 2019

The GW Compendium: A Practical Guide to Theoretical Photoemission Spectroscopy journal, July 2019

Bonding and Orientational Ordering of Long-Chain Carboxylic Acids on Cu(111): Investigations Using X-ray Absorption Spectroscopy journal, November 2001

Electronic and atomic structure of amorphous carbon journal, February 1987

Machine learning based interatomic potential for amorphous carbon journal, March 2017

SU-8 based pyrolytic carbon for the electrochemical detection of dopamine journal, January 2017

Understanding X-ray Spectroscopy of Carbonaceous Materials by Combining Experiments, Density Functional Theory, and Machine Learning. Part II: Quantitative Fitting of Spectra
journal, October 2019

Generalized Gradient Approximation Made Simple
journal, October 1996

Accurate absolute core-electron binding energies of molecules, solids, and surfaces from first-principles calculations
journal, October 2019

First Experimental Evidence of a C-1 s Core Exciton in Amorphous Carbon Films
journal, August 1995

Correlation between sp 3 -to-sp 2 Ratio and Surface Oxygen Functionalities in Tetrahedral Amorphous Carbon (ta-C) Thin Film Electrodes and Implications of Their Electrochemical Properties
journal, April 2016

A Chemical View on X-ray Photoelectron Spectroscopy: the ESCA Molecule and Surface-to-Bulk XPS Shifts
journal, December 2017

Structure of water adsorbed on the open Cu(110) surface: H-up, H-down, or both?
journal, October 2006

Connecting Dopant Bond Type with Electronic Structure in N-Doped Graphene
journal, July 2012

Spectroscopic observation of oxygen dissociation on nitrogen-doped graphene
journal, August 2017

Chemical bonding on surfaces probed by X-ray emission spectroscopy and density functional theory
journal, October 2004

An implementation of core level spectroscopies in a real space Projector Augmented Wave density functional theory code
journal, November 2011

Atomate: A high-level interface to generate, execute, and analyze computational materials science workflows
journal, November 2017

Hybrid carbon based nanomaterials for electrochemical detection of biomolecules
journal, July 2017

Electron transport determines the electrochemical properties of tetrahedral amorphous carbon (ta-C) thin films
journal, January 2017

On representing chemical environments
journal, May 2013

Amorphous carbon as a bio-mechanical coating — mechanical properties and biological applications
journal, February 2001

Periodic boundary conditions in ab initio calculations
journal, February 1995

Enhanced secondary electron yield from oxidized regions on amorphous carbon films studied by x-ray spectromicroscopy
journal, September 1999

Ab Initio Theory of Dynamical Core-Hole Screening in Graphite from X-Ray Absorption Spectra
journal, April 2005

Physisorption-Induced C-H Bond Elongation in Methane
journal, April 2006

Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method
journal, June 2010

XPS O 1s binding energies for polymers containing hydroxyl, ether, ketone and ester groups
journal, May 1991

Initial Fe ₃ O ₄ (100) Formation on Fe(100)
journal, May 2019

Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data
journal, February 2009

Integrated Carbon Nanostructures for Detection of Neurotransmitters
journal, June 2015

Initial Stages of Oxidation on Graphitic Surfaces: Photoemission Study and Density Functional Theory Calculations
journal, April 2009

Dynamical effects in x-ray absorption spectra of graphene and monolayered $h$ -BN on Ni(111)
journal, February 2010

Offset-corrected $Δ$ -Kohn-Sham scheme for semiempirical prediction of absolute x-ray photoelectron energies in molecules and solids
journal, July 2016

Electrochemical reactions of catechol, methylcatechol and dopamine at tetrahedral amorphous carbon (ta-C) thin film electrodes
journal, October 2015

A near edge X-ray absorption fine structure study of oxidized single crystal and polycrystalline diamond surfaces
journal, May 2014

Role of surface-electrical properties on the cell-viability of carbon thin films grown in nanodomain morphology
journal, May 2016

Reconstruction of the diamond (111) surface
journal, November 1992

X-ray absorption spectroscopy study of different solid carbon modifications
journal, July 1997

Observation of a C- $1 s$ Core Exciton in Diamond
journal, April 1985

Comparing molecules and solids across structural and alchemical space
journal, January 2016

On the Nature of Oxygen-Containing Surface Groups on Carbon Nanofibers and Their Role for Platinum Deposition—An XPS and Titration Study
journal, May 2009

Quantum confinement-induced tunable exciton states in graphene oxide
journal, July 2013

Structural Defects in Graphene
journal, November 2010

Automated generation and ensemble-learned matching of X-ray absorption spectra
journal, March 2018

Characterization and Electrochemical Properties of Oxygenated Amorphous Carbon (a-C) Films
journal, December 2016

A NEXAFS characterization of ion-beam-assisted carbon-sputtered thin films
journal, April 1995

Reactivity of Amorphous Carbon Surfaces: Rationalizing the Role of Structural Motifs in Functionalization Using Machine Learning
journal, September 2018

Electronic structure of graphite oxide and thermally reduced graphite oxide
journal, April 2011

Core level binding energies of functionalized and defective graphene
journal, January 2014

Intrinsic core level photoemission of suspended monolayer graphene
journal, July 2018

On the origin of core-level binding energy shifts
journal, December 1995

Special points for Brillouin-zone integrations
journal, June 1976

Multi-walled carbon nanotubes (MWCNTs) grown directly on tetrahedral amorphous carbon (ta-C): An interfacial study
journal, June 2015

Doping as a means to probe the potential dependence of dopamine adsorption on carbon-based surfaces: A first-principles study
journal, June 2017

Orientation of graphitic planes during the bias-enhanced nucleation of diamond on silicon: An x-ray absorption near-edge study
journal, November 1998

Calculation of the graphene C $1 s$ core level binding energy
journal, February 2015

Functional dependence of core-excitation energies
journal, December 2004

Calculations of near-edge x-ray-absorption spectra of gas-phase and chemisorbed molecules by means of density-functional and transition-potential theory
journal, September 1998

X-ray photoelectron spectroscopy: Progress and perspectives
journal, May 2010

Total Electron Yield Soft X-ray Absorption Spectroscopy in the C K Region of the Mixtures of Graphitic Carbons and Diamond for Quantitative Analysis of the sp ² /sp ³ -Hybridized Carbon Ratio
journal, June 2009

Efficient simulation of near-edge x-ray absorption fine structure (NEXAFS) in density-functional theory: Comparison of core-level constraining approaches
journal, February 2019

Diamond-like amorphous carbon
journal, May 2002

Tunable Magnetism in Carbon‐Ion‐Implanted Highly Oriented Pyrolytic Graphite
journal, December 2008

XPS determination of oxygen-containing functional groups on carbon-fibre surfaces and the cleaning of these surfaces
journal, October 1990

X-ray absorption spectroscopy (XAS) study of dip deposited a-C:H(OH) thin films
journal, August 2004

Overoxidation of carbon-fiber microelectrodes enhances dopamine adsorption and increases sensitivity
journal, January 2003

Carbon nanotube (CNT) forest grown on diamond-like carbon (DLC) thin films significantly improves electrochemical sensitivity and selectivity towards dopamine
journal, May 2015

High-throughput computational X-ray absorption spectroscopy
journal, July 2018

Thermal Stability and Reducibility of Oxygen-Containing Functional Groups on Multiwalled Carbon Nanotube Surfaces: A Quantitative High-Resolution XPS and TPD/TPR Study
journal, October 2008

Ab initio molecular simulations with numeric atom-centered orbitals
journal, November 2009

The effect of hydrogen on the electronic and bonding properties of amorphous carbon
journal, November 2006

The Structure of Graphite Oxide: Investigation of Its Surface Chemical Groups
journal, May 2010

Absolute Binding Energies of Core Levels in Solids from First Principles
journal, January 2017

Core-Level Binding Energies from GW : An Efficient Full-Frequency Approach within a Localized Basis
journal, August 2018

Atomic and electronic structure of tetrahedral amorphous carbon surfaces from density functional theory: Properties and simulation strategies
journal, October 2014

Computational Surface Chemistry of Tetrahedral Amorphous Carbon by Combining Machine Learning and Density Functional Theory
journal, September 2018

X-ray absorption near-edge structure calculations with the pseudopotentials: Application to the K edge in diamond and $α$ -quartz
journal, November 2002

Optimizing many-body atomic descriptors for enhanced computational performance of machine learning based interatomic potentials
journal, July 2019

The GW Compendium: A Practical Guide to Theoretical Photoemission Spectroscopy
journal, July 2019

Bonding and Orientational Ordering of Long-Chain Carboxylic Acids on Cu(111): Investigations Using X-ray Absorption Spectroscopy
journal, November 2001

Electronic and atomic structure of amorphous carbon
journal, February 1987

Machine learning based interatomic potential for amorphous carbon
journal, March 2017

SU-8 based pyrolytic carbon for the electrochemical detection of dopamine
journal, January 2017

The characterization of activated carbons with oxygen and nitrogen surface groups
journal, January 1997

Growth Mechanism and Origin of High $s p^{3}$ Content in Tetrahedral Amorphous Carbon
journal, April 2018