4.6 Article

Studies of Carbon Incorporation on the Diamond {100} Surface during Chemical Vapor Deposition using Density Functional Theory

Journal

JOURNAL OF PHYSICAL CHEMISTRY A
Volume 112, Issue 45, Pages 11436-11448

Publisher

AMER CHEMICAL SOC
DOI: 10.1021/jp8034538

Keywords

-

Funding

  1. EPSRC
  2. Element Six Ltd
  3. Naval Research Laboratory, Washington, D.C
  4. Moscow State University

Ask authors/readers for more resources

Accurate potential energy surface calculations are presented for many of the key steps involved in diamond chemical vapor deposition on the {100} surface (in its 2 x 1 reconstructed and hydrogenated form). The growing diamond surface was described by using a large (similar to 1500 atoms) cluster model, with the key atoms involved in chemical steps being described by using a quantum mechanical (QM, density functional theory, DFT) method and the bulk of the atoms being described by molecular mechanics (MM). The resulting hybrid QM/MM calculations are more systematic and/or at a higher level of theory than previous work on this growth process. The dominant process for carbon addition, in the form of methyl radicals, is predicted to be addition to a surface radical site, opening of the adjacent C-C dimer bond, insertion, and ultimate ring closure. Other steps such as insertion across the trough between rows of dimer bonds or addition to a neighboring dimer leading to formation of a reconstruction on the next layer may also contribute. Etching of carbon can also occur; the most likely mechanism involves loss of a two-carbon moiety in the form of ethene. The present higher-level calculations confirm that migration of inserted carbon along both dimer rows and chains should be relatively facile, with barriers of similar to 150 kJ mol(-1) when starting from suitable diradical species, and that this step should play an important role in establishing growth of smooth surfaces.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.6
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Chemistry, Organic

Pd-Catalyzed Ring Restructuring of Oxazolidines with Alkenes Leading to Fused Polycyclic Indolizines

Xianjun Xu, Huangdi Feng, Xiaoyong Zhang, Liangliang Song, Luc Van Meervelt, Johan Van der Eycken, Jeremy N. Harvey, Erik V. Van der Eycken

Summary: A palladium-catalyzed reaction for the synthesis of fused polycyclic indolizines has been developed. Experimental and theoretical studies suggest that the reaction involves C-C and C-O bond cleavage, providing a new approach for heterocycle synthesis.

ORGANIC LETTERS (2022)

Article Chemistry, Physical

Effect of solvent motions on the dynamics of the Diels-Alder reaction

Xiaoyong Zhang, Pierre-Louis Lefebvre, Jeremy N. Harvey

Summary: The solvent environment has minimal influence on transition state passage dynamics of the Diels-Alder reaction in aprotic solvents, with the notable effect occurring far from the transition state region where reactants are caged within the reactant well.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

Article Chemistry, Physical

Synthesis of Heterocycles via Aerobic Ni-Catalyzed Imidoylation of Aromatic 1,2-Bis-nucleophiles with Isocyanides

Julien Escudero, Pieter Mampuys, Carl Mensch, Charles B. Bheeter, Robby Vroemans, Romano V. A. Orru, Jeremy Harvey, Bert U. W. Maes

Summary: o-Phenylene N-substituted iminocarbonates can be obtained through aerobic Ni-catalyzed reaction of readily available catechols and isocyanides. The choice of oxidant and absence of base are crucial to avoid unwanted catechol oxidation. This method is generally applicable to other oxidation-sensitive aromatic 1,2-bisnucleophiles, providing a new approach to important bicyclic heterocycles.

ACS CATALYSIS (2022)

Article Chemistry, Multidisciplinary

Microscopic Reactivity of Phenylferrate Ions toward Organyl Halides

Stefan Lulf, Luxuan Guo, Tobias Parchomyk, Jeremy N. Harvey, Konrad Koszinowski

Summary: This study investigates the oxidative addition of organyl halides to phenylferrate anions in the gas phase, revealing the impact of different iron complexes on reactivity and reaction pathways. DFT calculations provide insights into the high reactivity of Ph2Fe(I)(-) complex.

CHEMISTRY-A EUROPEAN JOURNAL (2022)

Article Chemistry, Multidisciplinary

The Mechanism of Biochemical NO-Sensing: Insights from Computational Chemistry

Ahmed M. Rozza, Marcell Papp, Neil R. McFarlane, Jeremy N. Harvey, Julianna Olah

Summary: This study used a combination of theoretical tools to investigate various aspects of NO binding and reaction intermediates. The results suggest that NO binding leads to conformational changes in the protein.

CHEMISTRY-A EUROPEAN JOURNAL (2022)

Review Biochemistry & Molecular Biology

Electronic Absorption Spectroscopy and Photochemistry of Criegee Intermediates

Tolga N. Karsili, Barbara Marchetti, Marsha Lester, Michael N. R. Ashfold

Summary: This article reviews the current knowledge about the electronic spectroscopy of Criegee intermediates (CIs), with a focus on atmospherically relevant CIs and conjugated carbene-derived CIs of interest in synthetic chemistry. The article also summarizes the photochemical data reported to date, including studies on photo-induced fission of the terminal O-O bond and speculations about possible alternate decay processes for CIs following non-adiabatic coupling and dissociation.

PHOTOCHEMISTRY AND PHOTOBIOLOGY (2023)

Article Chemistry, Multidisciplinary

An automated method for graph-based chemical space exploration and transition state finding

Pablo Ramos-Sanchez, Jeremy N. Harvey, Jose A. Gamez

Summary: A novel algorithm is proposed to explore the chemical space by generating reaction networks using heuristics based on chemical theory. The algorithm improves performance by considering only transformations that break two chemical bonds and form two new ones. It estimates energy barriers using quantum chemical calculations and can also identify missed species during the previous step to further define the reaction network. The algorithm has successfully identified the most important reaction pathways in five different chemical reactions.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2023)

Article Chemistry, Physical

Iron-Catalyzed Kumada Cross-Coupling Reaction Involving Fe8Me12- and Related Clusters: A Computational Study

Andrea Daru, Carlos Martin-Fernandez, Jeremy N. Harvey

Summary: This article presents a mechanistic investigation of the iron-catalyzed Kumada reaction involving clusters as active species. It suggests that 11- and 13-coordinated clusters are fundamental for initiating the reaction, and proposes a classic initiation step.

ACS CATALYSIS (2022)

Article Chemistry, Physical

Quantifying the Cooperative Process of Molecular Self-Assembly on Surfaces: A Case Study of Isophthalic Acids

Tamara Rinkovec, Demian Kalebic, Mark Van der Auweraer, Wim Dehaen, Jeremy N. Harvey, Steven De Feyter

Summary: In this study, the effect of concentration on the self-assembled molecular network formation process was investigated using scanning tunneling microscopy. Isophthalic acids were chosen as a model system, and the adsorption behavior was evaluated at the nanoscale. The results showed the existence of a critical concentration for self-assembly, with the molecular structure having a significant impact on this threshold value. Furthermore, highly cooperative behavior was observed at the liquid/solid interface, providing a rare example of quantitative measurement of cooperative phenomena.

JOURNAL OF PHYSICAL CHEMISTRY C (2023)

Article Biochemistry & Molecular Biology

Stability profile of vimentin rod domain

Anastasia V. Lilina, Simon Leekens, Hani M. Hashim, Pieter-Jan Vermeire, Jeremy N. Harvey, Sergei V. Strelkov

Summary: Intermediate filaments (IFs) are essential components of the metazoan cytoskeleton, but their molecular architecture and assembly process are not fully understood. This study investigated the structure and stability of human vimentin, a model IF protein, and found that different regions of the protein have varying stability. These findings contribute to a better understanding of the molecular mechanisms driving IF assembly.

PROTEIN SCIENCE (2022)

Article Chemistry, Physical

Computational mechanistic analysis of a cationic Suzuki-Miyaura reaction without added base

Tolga Yaman, Jeremy N. N. Harvey

Summary: Novel density functional theory (DFT) calculations were performed to investigate the mechanism of a base-free Suzuki-Miyaura cross-coupling reaction with phosphine ligands. The results are consistent with experimental findings and suggest a mechanism involving recycling of the arylboronic acid moiety. Our calculations focus on the transmetalation and reductive elimination steps.

CATALYSIS SCIENCE & TECHNOLOGY (2023)

Article Chemistry, Physical

Machine Learning Representations of the Three Lowest Adiabatic Electronic Potential Energy Surfaces for the ArH2 + Reactive System

Maarten Konings, Jeremy N. Harvey, Jeïrome Loreau

Summary: In this work, Gaussian process regression machine learning representations of the three lowest coupled 2A' adiabatic electronic potential energy surfaces of the ArH2+ reactive system are presented. The nonadiabatic coupling matrix elements are also calculated. Accurate ab initio electronic structure calculations, taking into account the spin-orbit coupling, serve as input for the machine learning training process. The fitted potential energy surfaces show high accuracies, meeting the requirements for chemical dynamics at low temperature.

JOURNAL OF PHYSICAL CHEMISTRY A (2023)

Article Chemistry, Physical

Molecular photodissociation dynamics revealed by Coulomb explosion imaging

Stuart W. Crane, Jason W. L. Lee, Michael N. R. Ashfold, Daniel Rolles

Summary: Coulomb explosion imaging (CEI) methods are increasingly used to explore and distinguish the static stereo-configurations of small quantum systems. By using ultrafast laser pulses, CEI experiments can track the time-evolution of molecular structures and advance understanding of molecular fragmentation processes. This Perspective highlights two emerging families of dynamical studies: 'one-colour' studies and 'two-colour' studies, which provide new insights into molecular fragmentation processes and charge transfer processes with better stereochemical control.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2023)

Article Chemistry, Physical

Quantifying the Cooperative Process of Molecular Self-Assembly on Surfaces: A Case Study of Isophthalic Acids

Tamara Rinkovec, Demian Kalebic, Mark Van der Auweraer, Wim Dehaen, Jeremy N. Harvey, Steven De Feyter

Summary: This study investigates the effect of concentration on the self-assembly process of molecular networks using scanning tunneling microscopy. The research aims to improve the understanding of 2D supramolecular chemistry by obtaining quantitative data. The results show highly cooperative behavior and the significant impact of molecular structure on the critical concentration.

JOURNAL OF PHYSICAL CHEMISTRY C (2023)

Article Chemistry, Physical

Disentangling sequential and concerted fragmentations of molecular polycations with covariant native frame analysis

Joseph W. McManus, Tiffany Walmsley, Kiyonobu Nagaya, James R. Harries, Yoshiaki Kumagai, Hiroshi Iwayama, Michael N. R. Ashfold, Mathew Britton, Philip H. Bucksbaum, Briony Downes-Ward, Taran Driver, David Heathcote, Paul Hockett, Andrew J. Howard, Edwin Kukk, Jason W. L. Lee, Yusong Liu, Dennis Milesevic, Russell S. Minns, Akinobu Niozu, Johannes Niskanen, Andrew J. Orr-Ewing, Shigeki Owada, Daniel Rolles, Patrick A. Robertson, Artem Rudenko, Kiyoshi Ueda, James Unwin, Claire Vallance, Michael Burt, Mark Brouard, Ruaridh Forbes, Felix Allum

Summary: This study investigates the fragmentation dynamics of 1-iodopropane and 2-iodopropane after interaction with intense femtosecond laser pulses using experimental ion imaging. The resulting polycation fragments are analyzed using covariance imaging analysis, and contributions from three-body concerted and sequential fragmentation mechanisms are isolated. The angular distribution of the fragment ions is found to be more complex than previous studies, and differs significantly between the two isomeric species. Detailed physical insights into the fragmentation dynamics are obtained through simulations and analysis of the dissociation channels of interest.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

No Data Available