Example Of Dissertation Methodology On BN Doped Graphene: π - π Stacking

Chemistry

6. Cambridge Structural Database System
6.1 Introduction
Boron Nitride (BN) doped graphene is a nanostructure that is highly useful in many modern applications including in the health, computer, and electronic fields. The research proposed is to add the tri-coordinate form of the Boron atom to the graphene. The graphene is the conjugated framework that supports the BN doping. The purpose for the experiment is to improve the optical and electrical properties of the material. The improvements can enhance to performance for OFET transistors. The Cambridge Structural Database (CSD) in conjunction with the Mercury software applications will be used in order to identify the most suitable compounds that react with π -π stacking. The structural advantage of π -π stacking is essential, because π -π stacking exhibits the properties that can enhance electron transport and improve conductivity performance of the transistors.
6.1.1 The Cambridge Structural Database
The Cambridge Structural Database (CSD) system is indispensible to scientists who need to gain knowledge of small-molecule organic-organic and metal-organic crystal structures. The database is a rich source of physical and chemical properties for the molecules. The search and retrieval part of the database is the ConQuest software application. Mercury is the component of CSD that allows the user to download structures and manipulate their molecular structures. The most recent update is CSD v5.36 (2015) that was released on 15 February 2015. The CSD is updated periodically modifying and adding data to ConQuest and Mercury. In February 2015, CSD added CrystalWorks making the total number of entries into the database equals 1,172,330. Other databases that are integrated with the database system include Mogul, IsoStar, Relibase, and WebCSD. The additional structures added to the database enhance the ability of researchers to find needed structures that are not generally used.
6.1.2 History
The first crystal structure was the ‘zinc blende’; it was identified by W.L. and W. H. Bragg in 1912 and 1913. From that time until today, crystallography is a growing science that is important to many disciplines including medicines and computer applications. By 1916, crystallography data was already being compiled and in 1929 Linus Pauling used the gathered data to list “five rules for determining the structures of complex inorganic ionic crystals”. Organic structures became part of the databases because of x-ray crystallography. The data resulting from x-ray measurements added to the understanding about bond strengths, hydrogen bonds as well as interactions between synthetic and natural molecular structures. The Cambridge Crystallographic Data Centre (CCDC) in was opened in 1965, but the beginning of the centre was a year earlier when Olga Kennard was asked to create the centre. In 1965, the CSD system was developed specifically for education and research of chemical structures by allowing the student or researcher to manipulate the structure and view in 3-dimensions of crystal structures.
6.2 Mercury software application
The Mercury software application makes the data available on CSD even more valuable. The user is able to turn the structures around in order to view them from any aspect; an x-y-z grid can be added to the image so the proper framework is known at all times (figure A-1). Experimental data can be input so that a visual image of the results can be seen graphically. All asymmetrical atoms are termed ‘crystal chemical unit’ (c.c.u.) and the major number of molecules generated are asymmetric. At times a symmetrical atom is generated along the c.c.u. coordinates; the symmetry-generated atoms are tagged to show the relationship to generating the asymmetrical coordinates. The understanding of the chemical and physical influences of the structures is possible because 2- and 3-dimensional images are compiled in a theoretical bond-to-bond and atom-to-atom matching. The user can evaluate different structural options because the application allows atoms to be labeled, and the configuration for images includes stick-an-ball, wireframe or space-filled so visualization of how relationships between atoms is easy.
The Mercury application allows bonds can be depicted as ‘short contact ˂ sum of van der Waal’s radii’ that designate a weaker bond or as ‘H-bonds’ that are stronger. In 1987, researchers compiled tables of bond lengths that were measured by x-ray and neutron diffraction to prove the need for such tables to make the crystallographic database more practical to use. The CSD now contains a variety of physical properties measured by infrared and diffraction as well as other properties to make the database very convenient. The CSD is necessary in many researches and this study of BN (Boron Nitride) Doped Graphene: π - π stacking will use the database extensively.
6.3 Pi-Pi Stacking
Pi to pi stacking is also called π -π stacking or simply pi stacking in the literature. π -π stacking is the interaction between aromatic rings that is not attractive and is non-covalent. Electrostatic potential is an important unit in π -π stacking; for example, one aromatic ring with a positive and one aromatic ring with a negative electrostatic potential changes the configuration of the molecule. When two benzene rings are influenced by different electrostatic potential the whole molecule be T-shaped or parallel-displaced-shaped depending on the strengths of the potentials. Aromatic rings rarely show any overlap when the rings are in “face-to-face π –π alignment”. Janiak used the CSD and a literature review to evaluate the geometry in metal complexes with ligands containing aromatic nitrogen. The results showed that parallel-displaced rings (or slipped stacking).
6.4 Nano-structure
The reason π -π stacking is studied and evaluated for crystalline materials is because of its effect .on how crystals grow and therefore on the resulting solid state structure of the crystalline structure after it stops growing. The π -π stacking, hydrogen bonding C-H to pi and halogen bonding all influence crystalline growth and final structure.

6-5. Research Statement

The Mercury software application will be used in order to identify compounds that are impacted with π -π stacking. The structural advantage of π -π stacking is an essential characteristic for a successful research project; π -π stacking exhibits the properties that enhance electron transport and improve conductivity. The two properties of improved transport and conductivity are expected to greatly improve the performance of OFET transistors.
Figure 1Example of structures used for mechanism and modelling research
The research involves the searching through the CSD database in order to identify the most reliable and the most suitable compounds for transistors that interact in the π –π stacking. The first step is to search the database for C2B compounds and the second step is to search the database for C2BN compounds that are reliable and appropriate compounds to meet the purpose of the study. The best compounds that react with π –π stacking need to be identified for use in the construction of OFET transistors.
Crystallography is applied to many combined groups of materials that were not obviously compatible in 1912 when the first crystal structure was determined. The research will identify the knowledge gaps as well as offering a compilation of studies focused upon BN doping of graphene. The information is helpful in many fields because the use of graphene as a nano-material is ranges widely.
6.6 Research Design
The CSD and the Mercury application will be extensively used to compile the data on the BN doping of graphene and the π –π stacking. A literature review for BN doping graphene and similar topics will be carried out to knowledge for identifying the appropriate structures on the CSD. Peer-reviewed academic journals will be the references used to learn the research that is already available on the process of BN doping on graphene, especially for enhancing electron transfer and conductivity.

The research question is

“What is the influence of π –π stacking in the BN doping process of graphene?”
Mainly, Mercury will be used to learn the following information and compile the data listed below.
structural data and images
molecular electrostatic potential
nanostructure size

π –π stacking

total energy,
bond strengths,
and other data from the analyses available at CSD.

The results of the research will be reported, evaluated and recommendations will be made based on the findings.

6.7 Summary
The research question for the proposed study is “What is the influence of π –π stacking in the BN doping process of graphene?” The expected outcome of the research is to identify specific structures for improving OFET transistors. Mercury is the component of CSD that will be used in order to manipulate their molecular structures until the best choice or choices are identified. The structural advantage of π -π stacking is essential to exploit in the structure design, because π -π stacking exhibits the properties that can enhance electron transport and improve conductivity performance of OFET transistors. Electrostatic potential is an important unit in π -π stacking; for example, one aromatic ring with a positive and one aromatic ring with a negative electrostatic potential changes the configuration of the molecule. Improved electron transport and conductivity are expected to improve the performance of OFET transistors when the appropriate and reliable structure with π -π stacking is identified.
6.8 References
Allen FH. (2002) The Cambridge Structural Database: A quarter of a million crystal structures and rising. . Acta Crystallographic B58: 380-388.
Berseneva N, Krasheninnikov AV and Nieminen RM. (2011) Mechanisms of Postsynthesis Doping of Boron Nitride Nanostructures with Carbonfrom First-Principles Simulations. PHYSICAL REVIEW LETTERS. http://www.acclab.helsinki.fi/~akrashen/publ/PhysRevLett.107.035501.pdf
Centre CCD. The Cambridge Structural Data Base System: Research and Education. http://www.ccdc.cam.ac.uk/
CDS News – Structural Database System (2015) STFC Chemical Database, https://cds.dl.ac.uk/cgi-bin/news/disp?csds
Groom CR and Allen FH. (2014) The Cambridge Structural Database in retrospect and prospect. Angew Chem Int Ed Engl 53: 662-671.
Janiak C. (2000) A critical account on [small pi]-[small pi] stacking in metal complexes with aromatic nitrogen-containing ligands. Journal of the Chemical Society, Dalton Transactions: 3885-3896.
6.9 Appendices
6.9.1 Appendix 1
Figure A- 1 Theoretical structure on CSD x-y-z axis shows (Author)
6.10 Endnotes