Towards the matter compiler: looking ahead to computer-controlled molecular assembly

This thesis addresses the concept of atomically precise manufacturing and aims to examine some likely aspects of the necessary infrastructure and knowledge that will be required from a theoretical standpoint. By way of introduction, I trace the history of Science Fiction’s influence on scientific research and examine some examples that have specifically inspired the thinking behind nanoscience and nanotechnology. More serious speculation, both in favour of and arguing against the possibility of bottom-up manufacturing is also discussed. I look at two schools of thought; directed assembly, typified by the ambition to assemble molecular structures piece by piece and self assembly, where networks of molecules form into arrays on substrates, imparting novel properties. Various methodologies and tools available to the nanotechnologist are examined. Density functional theory, as employed in the AIMpro code, and Molecular Mechanics are discussed, particularly in respect of their strengths and weaknesses for use in simulating the kind of nanoscale processes appropriate to nanomanufacturing. The theoretical basis behind scanning tunneling microscopes is also examined, with particular attention paid to their potential for upscaling in the future. Some components found within scanning tunneling microscopes are simulated using Density Functional Theory. Models of pure tungsten tips are studied at various levels of complexity in order to decide upon a reasonable compromise between accuracy and ease of computation. The nature of the interlayer interaction in few layer graphenes is examined and pristine and defected graphitic surfaces, are studied with a view towards their use as nano-workbenches. Their images as produced in scanning tunneling microscopes are simulated. Density Functional Theory is applied to organic molecules self-assembling on metallic substrates. Specifically, tetracene on a clean copper surface and on an oxygen-terminated copper surface is studied. Finally, I discuss the significance of the results of each section, taken individually and as a whole, and try to put it into perspective regarding the practicality of actually employing this paradigm realistically in the near future

DESIGN OF GRAPHENE-BASED SENSORS FOR NUCLEIC ACIDS DETECTION AND ANALYSIS

DNA (Deoxyribonucleic Acid) is the blueprint of life as it encodes all genetic information. In genetic disorder such as gene fusion, Copy Number Variation (CNV), and single nucleotide polymorphism, Nucleic acids such as DNA bases detection and analysis is used as the gold standard for successful diagnosis. Researchers have been conducting rigorous studies to achieve genome sequences at low cost while maintaining high accuracy and high throughput. A quick, accurate, and low-cost DNA detection approach would revolutionize medicine. Genome sequence helps to enhance people’s perception of inheritance, disease, and individuality. This research aims to improve DNA bases detection accuracy, and efficiency, and reduce the production cost, thus novel based sensors were developed to detect and identify the DNA bases. This work aims at first to develop specialized field effect transistors which will acquire real-time detection for different concentrations of DNA. The sensor was developed with a channel of graphite oxide between gold electrodes on a substrate of a silicon wafer using Quantumwise Atomistix Toolkit (ATK) and its graphical user interfaces Virtual Nanolab (VNL). The channel was decorated with trimetallic nanoclusters that include gold, silver, and platinum which have high affinity to DNA. The developed sensor was investigated by both simulation and experiment. The second aim of this research was to analyze the tissue transcriptome through DNA bases detection, thus novel graphene-based sensors with a nanopore were designed and developed to detect the different DNA nucleobases (Adenine (A), Cytosine (C), Guanine (G), Thymine (T)). This research focuses on the simulation of charge transport properties for the developed sensors. This work includes experimental fabrication and software simulation studies of the electronic properties and structural characteristics of the developed sensors. Novel sensors were modeled using Quantumwise Atomistix Toolkit (ATK) and its graphical user Interface Virtual Nanolab (VNL) where several electronic properties were studied including transmission spectrum and electrical current of DNA bases inside the sensor’s nanopore. The simulation study resulted in a unique current for each of the DNA bases within the nanopore. This work suggests that the developed sensors could achieve DNA sequencing with high accuracy. The practical implementation of this work represents the ability to predict and cure diseases from the genetic makeup perspective

Bistability between π -diradical open-shell and closed-shell states in indeno[1,2- a ]fluorene

Indenofluorenes are non-benzenoid conjugated hydrocarbons that have received great interest owing to their unusual electronic structure and potential applications in nonlinear optics and photovoltaics. Here we report the generation of unsubstituted indeno[1,2-a]fluorene on various surfaces by the cleavage of two C–H bonds in 7,12-dihydroindeno[1,2-a]fluorene through voltage pulses applied by the tip of a combined scanning tunnelling microscope and atomic force microscope. On bilayer NaCl on Au(111), indeno[1,2-a]fluorene is in the neutral charge state, but it exhibits charge bistability between neutral and anionic states on the lower-workfunction surfaces of bilayer NaCl on Ag(111) and Cu(111). In the neutral state, indeno[1,2-a]fluorene exhibits one of two ground states: an open-shell π-diradical state, predicted to be a triplet by density functional and multireference many-body perturbation theory calculations, or a closed-shell state with a para-quinodimethane moiety in the as-indacene core. We observe switching between open- and closed-shell states of a single molecule by changing its adsorption site on NaCl

Rational Design of Metal-organic Electronic Devices: a Computational Perspective

Organic and organometallic electronic materials continue to attract considerable attention among researchers due to their cost effectiveness, high flexibility, low temperature processing conditions and the continuous emergence of new semiconducting materials with tailored electronic properties. In addition, organic semiconductors can be used in a variety of important technological devices such as solar cells, field-effect transistors (FETs), flash memory, radio frequency identification (RFID) tags, light emitting diodes (LEDs), etc. However, organic materials have thus far not achieved the reliability and carrier mobility obtainable with inorganic silicon-based devices. Hence, there is a need for finding alternative electronic materials other than organic semiconductors to overcome the problems of inferior stability and performance. In this dissertation, I research the development of new transition metal based electronic materials which due to the presence of metal-metal, metal-?, and ?-? interactions may give rise to superior electronic and chemical properties versus their organic counterparts. Specifically, I performed computational modeling studies on platinum based charge transfer complexes and d10 cyclo-[M(?-L)]3 trimers (M = Ag, Au and L = monoanionic bidentate bridging (C/N~C/N) ligand). The research done is aimed to guide experimental chemists to make rational choices of metals, ligands, substituents in synthesizing novel organometallic electronic materials. Furthermore, the calculations presented here propose novel ways to tune the geometric, electronic, spectroscopic, and conduction properties in semiconducting materials. In addition to novel material development, electronic device performance can be improved by making a judicious choice of device components. I have studied the interfaces of a p-type metal-organic semiconductor viz cyclo-[Au(µ-Pz)]3 trimer with metal electrodes at atomic and surface levels. This work was aimed to guide the device engineers to choose the appropriate metal electrodes considering the chemical interactions at the interface. Additionally, the calculations performed on the interfaces provided valuable insight into binding energies, charge redistribution, change in the energy levels, dipole formation, etc., which are important parameters to consider while fabricating an electronic device. The research described in this dissertation highlights the application of unique computational modeling methods at different levels of theory to guide the experimental chemists and device engineers toward a rational design of transition metal based electronic devices with low cost and high performance

On-surface synthesis of a doubly anti-aromatic carbon allotrope

Synthetic carbon allotropes such as graphene, carbon nanotubes and fullerenes have revolutionized materials science and led to new technologies. Many hypothetical carbon allotropes have been discussed, but few have been studied experimentally. Recently, unconventional synthetic strategies such as dynamic covalent chemistry and on-surface synthesis have been used to create new forms of carbon, including γ-graphyne, fullerene polymers, biphenylene networks and cyclocarbons. Cyclo[N]carbons are molecular rings consisting of N carbon atoms; the three that have been reported to date (N = 10, 14 and 18) are doubly aromatic, which prompts the question: is it possible to prepare doubly anti-aromatic versions? Here we report the synthesis and characterization of an anti-aromatic carbon allotrope, cyclo[16]carbon, by using tip-induced on-surface chemistry. In addition to structural information from atomic force microscopy, we probed its electronic structure by recording orbital density maps with scanning tunnelling microscopy. The observation of bond-length alternation in cyclo[16]carbon confirms its double anti-aromaticity, in concordance with theory. The simple structure of C16 renders it an interesting model system for studying the limits of aromaticity, and its high reactivity makes it a promising precursor to novel carbon allotropes

Simulation of Magnetic and Electronic Properties of Nanostructures

In the first part of this thesis I utilize density functional methods to simulate a previously unreported kind of single-molecule magnets with spin-crossover effect, which consist of a single 5d transition metal magnetic center adsorbed on a graphene nanoflake. In the second part I apply DFT to explain the stability of the [Au14(PPh3)8](NO3)4 nanocluster. The third part is dedicated to method development for electron transport simulation in mesoscopic two-dimensional nanodevices