Project

Computational chemistry for elucidating reaction mechanisms of graphene with relevant oxygen containing molecules

Goal: The project studies the reactivity of graphene sheets. Two main subtopics: a) Special effects seen at the edge of graphene layers and b) gas-graphene reaction (including NO, O2, H2O and CO2). This is done through computational chemistry.
----------------------------------------------------------------------------------------------------------------
Se pretende implementar computadores de alto rendimiento (HPC) para desarrollar investigación teórica sobre reacciones de combustión. Este proyecto fue ideado a partir de interrogantes surgidas en el trabajo de tesis de la investigadora principal y busca contestar preguntas fundamentales referentes a dos temas específicos: (a) efectos particulares observados ante la saturación de los bordes de grafeno y (b) el mecanismo de reacción de los NO con los bordes de la molécula de grafeno.

Date: 31 October 2017 - 30 October 2021

Updates
0 new
50
Recommendations
0 new
1
Followers
0 new
17
Reads
0 new
293

Project log

Andrea M. Oyarzún
added a research item
This study assesses the pedagogical benefits obtained by students, teachers, and a sponsor through the development of a computational chemistry research project on interactions between carbon materials and gases. Achievements, challenges, and opportunities are identified, emphasizing the mastery of transferable and technical skills throughout the four-year-long project. Engineering thesis students formed the teamwork. We highlight the implementation of the servers and software which are necessary to apply computational chemistry as a methodological tool. The subject of air pollution is also examined by performing a multidisciplinary analysis that determines potential areas for future applications and the impact of the computational analyses performed. It is concluded that there is development of training abilities in complex scientific-technological areas for both undergraduate and graduate students in a geographically isolated context that may limit performance.
Andrea M. Oyarzún
added 2 research items
Intrinsic reaction coordinate (IRC) data regarding the interactions of water with a carbene-like active site located at the edge of a polyaromatic hydrocarbon [[1], [2], [3]] has been obtained using density functional theory (DFT) and the 6-31g(d) basis set as implemented in the Gaussian 16 software [4]. The data is presented as two videos (frontal and lateral mechanism views) combining four consecutive IRC calculations corresponding to the four different transition states presented on “https://doi.org/10.1016/j.carbon.2020.01.011” [3] (Figure 6, side approach). These videos provide powerful insights on two key aspects: a) the rotational process that occurs during water adsorption and b) the hydrogen gas desorption process during water gasification of carbons.
Reactions of carbon and oxygen containing molecules, such as O2, NO, H2O and CO2, are ubiquitous on earth and the universe. Through ab initio calculations, we study the reactions of H2O and CO2 with small graphene clusters containing armchair edges, both H- and non-H terminated, and compare with studies of zigzag carbon edges interacting with oxygen-containing molecules. Our results highlight the differences between armchair and zigzag sites and our mechanistic comparisons regarding carbon reactions with H2O and CO2, identify similarities and differences on their reactivity. In the case of H2O, adsorption is favored over armchair sites exhibiting no rotational process and the H2 desorption step is favored over zigzag sites. Regarding the CO2 reaction, chemisorption is favored on zigzag sites. Several adsorption mechanisms lead to the formation of lactone groups as the most stable structures. A specific armchair CO desorption path for stable functional groups exists, agreeing with experimental reports, and thus completing our explanations for this reaction, previously limited to zigzag sites. Finally, the reaction over armchair sites leads to direct formation of pentagonal rings, without an active site deactivation process and with low activation energies. This deeper understanding provides further possibilities for improving the control of carbon-oxygen reactions. https://doi.org/10.1016/j.carbon.2022.02.048 For a limited time, this article can be downloaded here: https://authors.elsevier.com/a/1eqOk1zUASAMu
Andrea M. Oyarzún
added an update
During October I presented our pedagogical reflexion at the CIFCOM2021 conference.
A related article was also submitted, as well as another one related to carbons.
The manuscript sent to Carbon is ready now as a preprint: http://ssrn.com/abstract=3954417
Finally, financial, scientific, outreach and objectives reports were written and sent to the funding agency.
More details about the project can be found in the new website:
 
Andrea M. Oyarzún
added a research item
This is not an experiment but a dissemination leaflet about the project outcomes.
Andrea M. Oyarzún
added an update
The PI is working on the closure of the project: financial, outreach and scientific reports.
 
Andrea M. Oyarzún
added an update
A talk to the community was given on October 27th, 2021.
This talked was given for a limited amount of people from Puerto Natales, due to the pandemic.
The topics included were: carbon materials, computational chemistry and project activities.
This talk is planned to be repeated in the future for a wider audience.
 
Andrea M. Oyarzún
added an update
Unfortunately, the Carbon Conference was postponed twice due to the pandemic, both in 2020 and 2021.
However, it was possible to connect with other researchers working in the carbon material field through online meetings.
This allowed to participate in a series of meetings related to chemical issues.
Here you will find a summary about the activities that were attended to:
(A) Carbon 2020 was replaced by a short meeting organized by the American Carbon Society: Carbon Science & Technology In The Fight Against COVID-19, Thursday, July 16, 2020. Here professor Mauricio Terrones and other researchers had interesting discussions about the role of carbon materials in the fight against the pandemic.
(B) In 2020 and 2021 it was possible to attend to four Faraday Discussions meetings regarding important aspects of the chemistry field, which allowed to discuss topics with the researchers and to get a general overview of the current work done by the research community. The experience gained through these online meetings greatly impacted the work, perspectives and proposals planned through 2021.
a. Faraday Discussion Air Quality in Megacities. 17-20 November 2020. This meeting was interesting for this project as there were discussions about atmospheric problems including the formation of particles in the air, measurement techniques, interactions between chemicals in the air among many others.
b. Chemistry of 2-dimensional materials: beyond graphene Faraday Discussion. 23-25 November 2020. This online meeting allowed to meet worldwide leaders in the field like Andrea Ferrari and Prof. Klaus Müllen. It was posible to ask questions that are relevant for this project, regarding the interactions between graphene clusters.
c. Time-resolved imaging of photo-induced dynamics Faraday Discussion. 1 - 4 February 2021. This meeting allowed to have an overview of the advances in experimental imaging. The overall conference presented relevant information that has the potential to greatly improve the computational methods in the future.
d. Faraday Discussion: Reaction Mechanisms in Catalysis. 17-19 February 2021. This meeting had interesting Works using computational chemistry tools including kinetic Monte Carlo methods for studying reactions.
(C) 15th International Conference in Materials Chemistry (MC15). 12-15 July 2021. This meeting allowed to learn more about the work that in being done by the materials chemistry community.
(D) Series of Carbon Webinar. Organized by the technical comitte: A/Prof. Nigel Marks, Dr Irene Suarez-Martinez, Dr Jacob W. Martin, Dr Natalya Garcia, Keelan Powell. This series of webinar has replaced the lost Carbon meeting in 2021 and has offered a selection of talks on different topics related to carbon materials. A big thank you to Jacob W. Martin for participating actively in this activity and sharing with the carbon community.
 
Andrea M. Oyarzún
added an update
This year I am the supervisor of four undergraduate thesis. In September, the students Pablo Araya, Hugo Ramos, Boris Gomez and Diego Almonacid presented their advances to the Department of Chemical Engineering of the Universidad de Magallanes.
The topics of these theses include "Biomass gasification reactions for producing SNG", "Economical aspects for carbon materials fabrication", "Applications of ReaxFF" and "Hydrogen storage on carbon materials".
As more sustainable energy projects for producing hydrogen with the intense wind energy of the Magellanic lands, the Department has shifted priorities towards energy and hydrogen related projects.
Some of the students participated in a Computational chemistry workshop taught by Andrea Oyarzún to a doctoral program. The workshop is now an integral part of a course taught within the doctoral program on Sciences with mention in Chemistry of Natural Products or Molecular Biology (http://www.umag.cl/postgrados/?page_id=1617).
Additionally, Iván Ignacio Moya Barría provided support to the students, helping to plan and run calculations and teaching general concepts and tools used during the thesis work.
We consider the development of this workshop as an important milestone of the research project, which contributes to the objective of developing a research group on these topics.
 
Andrea M. Oyarzún
added an update
The next scientific article related to this project is almost ready to be submitted.
This month we are working to finalize this project. Iván Ignacio Moya Barría
 
Andrea M. Oyarzún
added an update
This project allowed us to access some books related to carbon materials and also to air pollution.
Our interest in applications of carbon materials to the abatement of NOx has led me to read this book:
Clearing the Air: The Beginning and the End of Air Pollution by Tim Smedley (https://www.goodreads.com/book/show/40653218-clearing-the-air)
In Patagonia, we use gas within houses. I am also interested in further studying the indoor air quality in our houses.
This book highlights the importance of breathing for our health as an activity that we do during all our lives:
Breath: The New Science of a Lost Art by James Nestor (https://www.goodreads.com/book/show/48890486-breath)
The interesting work of Jacob W. Martin on soot formation has inspired me to see the carbon-oxygen interactions not only to study combustion and gasification, but also, to think in the formation of products and their applications.
 
Andrea M. Oyarzún
added an update
In collaboration with Iván Ignacio Moya Barría and the MSc. Daniela Navarro-Perez, we have written a pedagogical reflexion on the advantages, disadvantages, achievements and opportunities for the development of transferable skills on the students.
This work focuses on the benefits experienced by students, teachers/researchers and the institution, highlighting the main problems that we faced and how we solved them.
In particular, the development of a workshop for both postgraduate and undergraduate students was the best way to overcome the problems faced by the project, offering interesting development opportunities in the future.
This work will be presented at the CIFCOM2021 conference (https://cifcom.com). We hope to transform this work into a publication.
 
Andrea M. Oyarzún
added an update
The student Maria Ruiz has recently presented her undergraduate thesis to become a Chemistry and Environmental Engineer.
Her work consisted in performing a review of the NOx pollution in Chile and compare with statistical data about diseases on the respiratory system of the chilean population.
The work also included a review of abatement techniques and a proposal for localized solutions for selected areas of Chile.
 
Andrea M. Oyarzún
added an update
A brief workshop on Computational Chemistry has been developed and taught to postgraduate students from the Doctorate program on Sciences. Undergraduate thesis students working on topics related to this project has been invited to participate of the workshop.
The workshop has now been included in a course of the Doctorate program.
Six PhD students and two undergraduate students has successfully participated of this short workshop.
On 2020 the workshop was oriented to applications on enzymatic activity, whereas on 2021 it was oriented to general applications.
 
Andrea M. Oyarzún
added an update
The pandemic affected this project. An extension of the duration of the project of one year has been approved by the funding agency.
 
Andrea M. Oyarzún
added an update
The last article or this project is available for free until May 27:
Also the joint article:
 
Andrea M. Oyarzún
added 2 research items
This paper explores the reactivity differences for H2 adsorption/desorption processes at both edges and surfaces of curved and non-curved carbon materials. It was presented as an oral presentation at the Carbon 2019 conference, and the paper can be found on: http://carbon2019.org/wp-content/uploads/2019/07/246-oyarzun.pdf
This is a preprint of an article in press. To see the finished article please visit: https://doi.org/10.1016/j.carbon.2020.01.011 Free full article until May 27: https://authors.elsevier.com/a/1asaP1zUALh1L
Andrea M. Oyarzún
added an update
The undergraduate students, Catalina Gottschalk and Ivan Moya, participated on the annual Explora week at the university.
 
Andrea M. Oyarzún
added an update
On August 29th, a computational chemistry presentation was held at the Punta Arenas School to 14-15 years old students. The topic was quantum chemistry, with a focus on the activities that a researcher does.
 
Andrea M. Oyarzún
added an update
After leaving Loughborough, a visit to the Computational Modelling Group of the Department of Chemical Engineering and Biotechnology of the University of Cambridge followed. A successful meeting with the Research students Jacob Martin and Angiras Menon took place.
 
Andrea M. Oyarzún
added an update
On the 24th of July, after the Carbon 2019 conference, a journey to visit the United Kingdom was planned. Several activities took place, such a visit to the Chemistry Department of the Loughborough University were the physicists group headed by PhD R. Smith and PhD K. Jolley is stablished. The stay in Loughborough also included a short visit to the old house of Newton where we could see some nanotubes and their optical characteristics among other things.
 
Andrea M. Oyarzún
added an update
Also, different meetings with collaborators such as professors L. Radovic, J. Rodríguez-Mirasol and F. Vallejos-Burgos took place.
 
Andrea M. Oyarzún
added an update
Two studies co-authored with students were presented. An oral presentation attracted attention of different participants of the conference. The title of the presentation was "Curvature effects on the reactivity of nanomaterials" and the student that collaborated with this study is Iván Moya.
The chairman (in the picture) was C. Kulaots.
 
Andrea M. Oyarzún
added an update
Two studies co-authored with students were presented. In continuity to the study regarding graphene reactions with H2O and CO2 on zigzag sites presented on the Carbon 2018 conference, a new complementary study was presented as a poster, but this time focusing on armchair sites.
The title of the poster is "Graphene reactions with water and carbon dioxide on armchair sites" and the student that collaborated with this study is Catalina Gottschalk.
 
Andrea M. Oyarzún
added an update
With the help of D. B., the new server called mozart is now available. This server has the same specifications as martin (48C and 256 GB RAM), but 2 SSD drives of 1 Tb.
We do hope Mozart could make some beautiful music for our ears! Christopher D Latham Fernando Vallejos-Burgos
 
Andrea M. Oyarzún
added an update
Professor José Rodríguez-Mirasol from University of Málaga has been added as a new collaborator. He will visit the University of Magallanes in January 2019, with the purpose of presenting his work and participating in several meetings.
 
Andrea M. Oyarzún
added a research item
Aiming to better understand the reactivity of graphene-based materials, the present work employs density functional theory that provides detailed information about spin-density distributions for single and contiguous pairs of carbene-like active sites. In order to examine the extent to which different models, methodologies, and approximations affect the outcome, our calculations employ the AIMPRO, QuantumEspresso and Gaussian program packages. Models are in the form of polycyclic aromatic hydrocarbons (PAHs) and graphene nanoribbons (GNRs), both isolated and within supercells with periodic boundary conditions. Benchmarking calculations for the phenyl radical and cation are also presented. General agreement is found among the methods and also with previous studies. A significant electron spin polarization (spin density >1.096 electron spin) on the active sites is seen in both periodic and cluster systems, but it tends to be lower for GNRs than graphene clusters. The effect of the functional seems to be much more important than the position of singularities at the edges of the GNRs. Finally, we show the interactions and effects on spin density when a single site lies at the edge of a bilayer GNR, where bonding between layers may occur under specific circumstances.
Andrea M. Oyarzún
added 2 research items
H2O and CO2 reactions with graphene are of great interest in the energy industry as well as in materials related applications. Although the reactions may seem straightforward, their mechanistic details deserve further scrutiny, especially regarding to the reactants adsorption and products desorption steps. In this study we use quantum chemistry on zigzag actives sites to present thermodynamics and kinetics of the relevant mechanistic steps, and compare them with the previously studied NO and O2 reactions (Oyarzún 2016). Their differences and similarities are reviewed within the scope of oxygen transfer reactions for carbon materials. The mechanistic analysis of the water reaction results differ from the usually accepted mechanism, including dissociative adsorption instead of a concerted adsorption step with simultaneous H2 desorption. Additionally, a surface rearrangement for desorption of products is proposed, which may account for the inhibition process. In the case of CO2, inhibition mechanisms are also analysed. The results allow us to propose the participation of a surface or extended-edge effect on the inhibition process, which may account for experimental facts such as the hexagonal pits seen for the H2O and graphene reaction, in contrast to the circular ones seen for the CO2 and graphene reaction (Yang 1983). (1) Oyarzún, A.M., A.J.A. Salgado-Casanova, X. García and L.R. Radovic, Carbon, 2016. 99: 472-484. (2) Yang, R.T. and C. Wong, Journal of Catalysis, 1983. 82: 245-251.
The reaction of carbon materials with nitric oxide has gained increasing importance for both fundamental and practical reasons. The removal of NOx from stationary and mobile sources, smog reduction and the development of new NO sensors represent a few examples. In previous studies, we used computational chemistry to calculate thermochemical and kinetic information, and proposed a reaction route that connects the reactants and products through the N2O intermediate. In contrast, the present work proposes a reinterpretation of the mentioned kinetic results, and finds a different reaction mechanism may connect reactants and products through the NO2 intermediate. Hitherto overlooked experimental evidence seen during NO chemisorption on cellulosic chars (DeGroot, 1991) appears to agree with this mechanism proposal and shows that further studies are required to both: a) clarify the role of the NO2 as an intermediate in the NO-carbon reaction and b) analyze the potential use of this reaction path to transform NO into N2 and O2. The latter involves the use of carbon as a catalyst in a key reaction mechanism, which supposes a mayor challenge for NOx remediation for environmental purposes.
Andrea M. Oyarzún
added an update
The server is operative and the software is running under SSE instructions. We hope we could enable AVX2 instructions sometime in the future.
 
Andrea M. Oyarzún
added an update
Dr. Fernando Vallejos-Burgos and PhD Christopher D Latham have been added as collaborators to this project. We are working to define the proper equipment to run calculations. Valuable suggestions has been made by Christopher D Latham.
 
Andrea M. Oyarzún
added a project goal
The project studies the reactivity of graphene sheets. Two main subtopics: a) Special effects seen at the edge of graphene layers and b) gas-graphene reaction (including NO, O2, H2O and CO2). This is done through computational chemistry.
----------------------------------------------------------------------------------------------------------------
Se pretende implementar computadores de alto rendimiento (HPC) para desarrollar investigación teórica sobre reacciones de combustión. Este proyecto fue ideado a partir de interrogantes surgidas en el trabajo de tesis de la investigadora principal y busca contestar preguntas fundamentales referentes a dos temas específicos: (a) efectos particulares observados ante la saturación de los bordes de grafeno y (b) el mecanismo de reacción de los NO con los bordes de la molécula de grafeno.