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Chemistry Theses and Dissertations

Theses/dissertations from 2023 2023.

aPKCs role in Neuroblastoma cell signaling cascades and Implications of aPKCs inhibitors as potential therapeutics , Sloan Breedy

Protein Folding Kinetics Analysis Using Fluorescence Spectroscopy , Dhanya Dhananjayan

Affordances and Limitations of Molecular Representations in General and Organic Chemistry , Ayesha Farheen

Institutional and Individual Approaches to Change in Undergraduate STEM Education: Two Framework Analyses , Stephanie B. Feola

Applications in Opioid Analysis with FAIMS Through Control of Vapor Phase Solvent Modifiers , Nathan Grimes

Synthesis, Characterization, and Separation of Loaded Liposomes for Drug Delivery , Sandra Khalife

Supramolecular Architectures Generated by Self-assembly of Guanosine and Isoguanosine Derivatives , Mengjia Liu

Syntheses, Photophysics, & Application of Porphyrinic Metal-Organic Frameworks , Zachary L. Magnuson

Chemical Analysis of Metabolites from Mangrove Endophytic Fungus , Sefat E Munjerin

Synthesis of Small Molecule Modulators of Non-Traditional Drug Targets , Jamie Nunziata

Synthetic Studies of Potential New Ketogenic Molecules , Mohammad Nazmus Sakib

Coupling Chemical and Genomic Data of Marine Sediment-Associated Bacteria for Metabolite Profiling , Stephanie P. Suarez

Enhanced Methods in Forensic Mass Spectrometry for Targeted and Untargeted Drug Analysis , Dina M. Swanson

Investigation of Challenging Transformations in Gold Catalysis , Qi Tang

Diazirines and Oxaziridines as Nitrogen Transfer Reagents in Drug Discovery , Khalilia C. Tillett

Developing New Strategy toward Ruthenium and Gold Redox Catalysis , Chenhuan Wang

Gold-Catalyzed Diyne-ene Cyclization: Synthesis of Hetero Polyaromatic Hydrocarbons and 1,2-Dihydropyridines , Jingwen Wei

Development of Antiviral Peptidomimetics , Songyi Xue

Theses/Dissertations from 2022 2022

Investigating a Potential STING Modulator , Jaret J. Crews

Exploring the Structure and Activity of Metallo-Tetracyclines , Shahedul Islam

Metabolomic Analysis, Identification and Antimicrobial Assay of Two Mangrove Endophytes , Stephen Thompson

Bioactivity of Suberitenones A and B , Jared G. Waters

Developing Efficient Transition Metal Catalyzed C-C & C-X Bond Construction , Chiyu Wei

Measurement in Chemistry, Mathematics, and Physics Education: Student Explanations of Organic Chemistry Reaction Mechanisms and Instructional Practices in Introductory Courses , Brandon J. Yik

Study on New Reactivity of Vinyl Gold and Its Sequential Transformations , Teng Yuan

Study on New Strategy toward Gold(I/III) Redox Catalysis , Shuyao Zhang

Theses/Dissertations from 2021 2021

Design, Synthesis and Testing of Bioactive Peptidomimetics , Sami Abdulkadir

Synthesis of Small Molecules for the Treatment of Infectious Diseases , Elena Bray

Social Constructivism in Chemistry Peer Leaders and Organic Chemistry Students , Aaron M. Clark

Synthesizing Laccol Based Polymers/Copolymers and Polyurethanes; Characterization and Their Applications , Imalka Marasinghe Arachchilage

The Photophysical Studies of Transition Metal Polyimines Encapsulated in Metal Organic Frameworks (MOF’s) , Jacob M. Mayers

Light Harvesting in Photoactive Guest-Based Metal-Organic Frameworks , Christopher R. McKeithan

Using Quantitative Methods to Investigate Student Attitudes Toward Chemistry: Women of Color Deserve the Spotlight , Guizella A. Rocabado Delgadillo

Simulations of H2 Sorption in Metal-Organic Frameworks , Shanelle Suepaul

Parallel Computation of Feynman Path Integrals and Many-Body Polarization with Application to Metal-Organic Materials , Brant H. Tudor

The Development of Bioactive Peptidomimetics Based on γ-AApeptides , Minghui Wang

Investigation of Immobilized Enzymes in Confined Environment of Mesoporous Host Matrices , Xiaoliang Wang

Novel Synthetic Ketogenic Compounds , Michael Scott Williams

Theses/Dissertations from 2020 2020

Biosynthetic Gene Clusters, Microbiomes, and Secondary Metabolites in Cold Water Marine Organisms , Nicole Elizabeth Avalon

Differential Mobility Spectrometry-Mass spectrometry (DMS-MS) for Forensic and Nuclear-Forensic applications , Ifeoluwa Ayodeji

Conversion from Metal Oxide to MOF Thin Films as a Platform of Chemical Sensing , Meng Chen

Asking Why : Analyzing Students' Explanations of Organic Chemistry Reaction Mechanisms using Lexical Analysis and Predictive Logistic Regression Models , Amber J. Dood

Development of Next-Generation, Fast, Accurate, Transferable, and Polarizable Force-fields for Heterogenous Material Simulations , Adam E. Hogan

Breakthroughs in Obtaining QM/MM Free Energies , Phillip S. Hudson

New Synthetic Methodology Using Base-Assisted Diazonium Salts Activation and Gold Redox Catalysis , Abiola Azeez Jimoh

Development and Application of Computational Models for Biochemical Systems , Fiona L. Kearns

Analyzing the Retention of Knowledge Among General Chemistry Students , James T. Kingsepp

A Chemical Investigation of Three Antarctic Tunicates of the Genus Synoicum , Sofia Kokkaliari

Construction of Giant 2D and 3D Metallo-Supramolecules Based on Pyrylium Salts Chemistry , Yiming Li

Assessing Many-Body van der Waals Contributions in Model Sorption Environments , Matthew K. Mostrom

Advancing Equity Amongst General Chemistry Students with Variable Preparations in Mathematics , Vanessa R. Ralph

Sustainable Non-Noble Metal based Catalysts for High Performance Oxygen Electrocatalysis , Swetha Ramani

The Role of aPKCs and aPKC Inhibitors in Cell Proliferation and Invasion in Breast and Ovarian Cancer , Tracess B. Smalley

Development of Ultrasonic-based Ambient Desorption Ionization Mass Spectrometry , Linxia Song

Covalent Organic Frameworks as an Organic Scaffold for Heterogeneous Catalysis including C-H Activation , Harsh Vardhan

Optimization of a Digital Ion Trap to Perform Isotope Ratio Analysis of Xenon for Planetary Studies , Timothy Vazquez

Multifunctional Metal-Organic Frameworks (MOFs) For Applications in Sustainability , Gaurav Verma

Design, Synthesis of Axial Chiral Triazole , Jing Wang

The Development of AApeptides , Lulu Wei

Chemical Investigation of Floridian Mangrove Endophytes and Antarctic Marine Organisms , Bingjie Yang

Theses/Dissertations from 2019 2019

An Insight into the Biological Functions, the Molecular Mechanism and the Nature of Interactions of a Set of Biologically Important Proteins. , Adam A. Aboalroub

Functional Porous Materials: Applications for Environmental Sustainability , Briana Amaris Aguila

Biomimetic Light Harvesting in Metalloporphyrins Encapsulated/Incorporated within Metal Organic Frameworks (MOFs). , Abdulaziz A. Alanazi

Design and Synthesis of Novel Agents for the Treatment of Tropical Diseases , Linda Corrinne Barbeto

Effect of Atypical protein kinase C inhibitor (DNDA) on Cell Proliferation and Migration of Lung Cancer Cells , Raja Reddy Bommareddy

The Activity and Structure of Cu2+ -Biomolecules in Disease and Disease Treatment , Darrell Cole Cerrato

Simulation and Software Development to Understand Interactions of Guest Molecules inPorous Materials , Douglas M. Franz

Construction of G-quadruplexes via Self-assembly: Enhanced Stability and Unique Properties , Ying He

The Role of Atypical Protein Kinase C in Colorectal Cancer Cells Carcinogenesis , S M Anisul Islam

Chemical Tools and Treatments for Neurological Disorders and Infectious Diseases , Andrea Lemus

Antarctic Deep Sea Coral and Tropical Fungal Endophyte: Novel Chemistry for Drug Discovery , Anne-Claire D. Limon

Constituent Partitioning Consensus Docking Models and Application in Drug Discovery , Rainer Metcalf

An Investigation into the Heterogeneity of Insect Arylalkylamine N -Acyltransferases , Brian G. O'Flynn

Evaluating the Evidence Base for Evidence-Based Instructional Practices in Chemistry through Meta-Analysis , Md Tawabur Rahman

Role of Oncogenic Protein Kinase C-iota in Melanoma Progression; A Study Based on Atypical Protein Kinase-C Inhibitors , Wishrawana Sarathi Bandara Ratnayake

Formulation to Application: Thermomechanical Characterization of Flexible Polyimides and The Improvement of Their Properties Via Chain Interaction , Alejandro Rivera Nicholls

The Chemical Ecology and Drug Discovery Potential of the Antarctic Red Alga Plocamium cartilagineum and the Antarctic Sponge Dendrilla membranosa , Andrew Jason Shilling

Synthesis, Discovery and Delivery of Therapeutic Natural Products and Analogs , Zachary P. Shultz

Development of α-AA peptides as Peptidomimetics for Antimicrobial Therapeutics and The Discovery of Nanostructures , Sylvia E. Singh

Self-Assembly of 2D and 3D Metallo-Supramolecules with Increasing Complexity , Bo Song

The Potential of Marine Microbes, Flora and Fauna in Drug Discovery , Santana Alexa Lavonia Thomas

Design, Synthesis, and Self-Assembly of Supramolecular Fractals Based on Terpyridine with Different Transition Metal Ions , Lei Wang

Theses/Dissertations from 2018 2018

Fatty Acid Amides and Their Biosynthetic Enzymes Found in Insect Model Systems , Ryan L. Anderson

Interrogation of Protein Function with Peptidomimetics , Olapeju Bolarinwa

Characterization of Nylon-12 in a Novel Additive Manufacturing Technology, and the Rheological and Spectroscopic Analysis of PEG-Starch Matrix Interactions , Garrett Michael Craft

Synthesis of Novel Agents for the treatment of Infectious and Neurodegenerative diseases , Benjamin Joe Eduful

Survey research in postsecondary chemistry education: Measurements of faculty members’ instructional practice and students’ affect , Rebecca E. Gibbons

Design, Synthesis, Application of Biodegradable Polymers , Mussie Gide

Conformational Fluctuations of Biomolecules Studied Using Molecular Dynamics and Enhanced Sampling , Geoffrey M. Gray

Analysis and New Applications of Metal Organic Frameworks (MOF): Thermal Conductivity of a Perovskite-type MOF and Incorporation of a Lewis Pair into a MOF. , Wilarachchige D C B Gunatilleke

Chemical Investigation of Bioactive Marine Extracts , Selam Hagos

Optimizing Peptide Fractionation to Maximize Content in Cancer Proteomics , Victoria Izumi

Germania-based Sol-gel Coatings and Core-shell Particles in Chromatographic Separations , Chengliang Jiang

Synthesis, Modification, Characterization and Processing of Molded and Electrospun Thermoplastic Polymer Composites and Nanocomposites , Tamalia Julien

Studies Aimed at the Synthesis of Anti-Infective Agents , Ankush Kanwar

From Florida to Antarctica: Dereplication Strategies and Chemical Investigations of Marine Organisms , Matthew A. Knestrick

Sorbent Enrichment Performance of Aromatic Compounds from Diluted Liquid Solution , Le Meng

Development of Bioactive Peptidomimetics , Fengyu She

Azamacrocyclic-based Frameworks: Syntheses and Characterizations , Chavis Andrew Stackhouse

Structure-based Design, Synthesis and Applications of a New Class of Peptidomimetics: 'Y -AA Peptides and Their Derivatives , Ma Su

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Thesis Preparation

The following information is provided to assist Chemistry graduate students as they prepare their theses. If graduate students have any questions that are not answered by this guide, they should email the Chemistry Education Office (questions about department policies) or MIT Libraries (for questions about thesis formatting, etc.)

Degree candidates must fill out the Degree Application via WebSIS at the start of the term. Important dates and deadlines (including late fees) for the upcoming academic year are listed below.  It is strongly advised that degree candidates apply for the degree list even if there is uncertainty about completing the thesis defense and submission by the  deadline, as there are no penalties for being removed from the degree list.

Students must successfully complete the thesis defense before submitting their final, signed thesis.

**Please note that the Specifications for Thesis Preparation were updated in November 2022. Please make sure you use these new guidelines.**

Important Dates & Deadlines

September 2023 degree list.

• Degree Application Deadline: June 16, 2023 ($50 late fee if submitted after this date, $85 late fee if submitted after July 21, 2023)
• Thesis Title Deadline:July 21, 2023 ($85 late fee if submitted after this date. If your thesis title is not finalized by this date, please enter your current working title and the final title can be updated later)
• Thesis Submission Deadline: August 18, 2023
• Last day of work in the lab: on or before August 31, 2023. If you plan to end your RA appointment earlier than August 31, 2023, please contact Jennifer to review your timeline.
• Your degree will officially be conferred by MIT on September 20, 2023
• Information about the MIT Health Plan and graduation will be available online here.

February 2024 Degree List

• Degree Application Deadline: September 8, 2023 ($50 late fee if submitted after this date, $85 late fee if submitted after December 15, 2022)
• Thesis Title Deadline: December 15, 2023 ($85 late fee if submitted after this date. If your thesis title is not finalized by this date, please enter your current working title and the final title can be updated later)
• Thesis Submission Deadline: January 19, 2024
• Last day of work in the lab: on or before January 15, 2024. If you plan to end your RA appointment earlier than January 15, 2024, please contact Jennifer to review your timeline.
• Your degree will officially be conferred by MIT on February 21, 2024

May 2024 Degree List

• Degree Application Deadline: February 9, 2024 ($50 late fee if submitted after this date, $85 late fee if submitted after April 12, 2024)
• Thesis Title Deadline: April 12, 2024 ($85 late fee if submitted after this date. If your thesis title is not finalized by this date, please enter your current working title and the final title can be updated later)
• Thesis Submission Deadline: May 10, 2024
• Last day of work in the lab: on or before May 29, 2024. If you plan to end your RA appointment earlier than May 29, 2024, please contact Jennifer to review your timeline.
• Your degree will officially be conferred by MIT on May 30, 2024

Scheduling your Thesis Defense

All PhD candidates must have a Thesis Defense. As soon as your defense is finalized, please email the Chemistry Education Office with the date, time, location, and thesis title . Thesis defenses are strongly encouraged to be in-person.  If there are questions or concerns about an in-person defense, please reach out to Jennifer Weisman. When thesis defenses are on campus, we recommend reserving a room once the defense date is finalized, student can reserve department rooms through the online scheduling system or request a classroom via this form .

Degree candidates should provide their advisor with a copy of the thesis at least two weeks before the defense and provide their thesis committee chair and member with a copy at least one week before the defense. However, degree candidates should talk with their advisor, committee chair, and committee member to find out if they need the thesis further in advance or if there are preferred formats. Degree candidates should allow time in between their thesis defense and the submission deadline to make edits and submit the final copies.

Please note that most receiving a PhD degree are required to present a seminar as part of the thesis defense. This seminar is open to the department. The degree candidate is responsible for providing the Chemistry Education Office with information about their thesis defense at least two weeks ahead of time. Following the seminar, the candidate will meet privately with the thesis committee.

Thesis Formatting

The Institute has very specific requirements for thesis preparation, which were updated in November 2022. Specifications for Thesis Preparation is available on the library’s website and should be read very carefully. The MIT Thesis FAQ may answer additional questions and a helpful checklist is also provided. The specifications also include information about copyright and use of previously published material in a thesis . Do  not  rely on any templates or prior theses from your research group – they may not reflect the most current guidelines. We have highlighted some especially important points below.

Font & Spacing

Title page & committee signature page.

• The title page of the first copy will be digitally signed by the author, advisor, and Professor Adam Willard. The title page should contain the title, name of the author, previous degrees, the degree(s) to be awarded at MIT, the date the degree(s) will be conferred (May, September, or February only), copyright notice, and appropriate names and signatures. Degrees are awarded in Chemistry, regardless of your specific research area. Regardless of when you defend or submit your thesis, the date of degree conferral must be May/June, September, or February.
• As noted above, the title page will be signed by you, your advisor, and Professor Willard. You do not need to have Professor Willard digitally sign the thesis before you submit it, we will arrange to have him sign it. If your advisor has a title (ex., Firmenich Professor of Chemistry) it should also be included under their name. If you are not sure if they have a title, you can consult the Faculty Directory . Professor Willard should have the following listed under his name, on two separate lines: Professor of Chemistry; Graduate Officer
• Each student should place the appropriate copyright notice on the thesis title page. Copyright notice consists of four elements: the symbol “c” with a circle around it © and/or the word “copyright”; the year of publication (the year in which the degree is to be awarded); the name of the copyright owner; the words “All rights reserved” or your chosen Creative Commons license. All theses should have the following legend statement exactly: The author hereby grants to MIT a nonexclusive, worldwide, irrevocable, royalty-free license to exercise any and all rights under copyright, including to reproduce, preserve, distribute and publicly display copies of the thesis, or release the thesis under an open-access license. Please carefully review the copyright information to determine the appropriate copyright ownership.
• The date under Signature of Author should be the date the final thesis is signed and submitted to the department.
• The title page is always considered to be page 1, and every page must be included in the count regardless of whether a number would be physically printed on a page. We recommend that you do not include the page number on the title page.
• There is also a signature page that will be digitally signed by your entire thesis committee. Your advisor will digitally sign your thesis twice, on the title page and signature page. The signature page is right after the title page.
• More details about digital signatures are provided below.

Table of Contents

Final thesis submission, general submission process.

Please carefully review the details below, including the file naming format . There are two steps to the final submissions process:

1. Submit the following documents to the Department of Chemistry:

• An electronic copy of your thesis in PDF/A-1 format (with no signatures)
• A PDF of the digitally signed title page and committee signature page (using DocuSign to obtain signatures)

Please send an email to your advisor, Jennifer Weisman, and William McCoy, which includes the 2 PDFs above and the following text:

“Dear Professor/Dr X: Attached is the final version of my thesis. Please use reply-all to this message to indicate your acceptance of my thesis document and your recommendation for certification by my department.”

**Note: if your thesis document is too large to send via email, your email can include a link to access the document via Dropbox, Google Drive, etc.**

2. Submit your thesis information to MIT Libraries here . Choose to opt-in or opt-out of ProQuest license and publication.  Include the same copyright and license information that is on your thesis title page. Note: this does not involve submitting your actual thesis.

Details for Thesis Submission Process

• After the defense, the student and thesis committee reach agreement on the final thesis document.
• Students should follow the format specifications as stated in the Specifications for Thesis Preparation . Do not print or physically sign pages.
• Students will have the thesis signed electronically through DocuSign. This process is described in detail in the section below.
• The title page is always considered to be page 1, and every page must be included in the count regardless of whether a number is physically printed on a page. The entire thesis (including title page, prefatory material, illustrations, and all text and appendices) must be paginated in one consecutive numbering sequence. Your committee signature page should be page 2. Please see the  Sample Title Page and committee signature page for reference.
• You will still include the title page and committee signature page in the full thesis PDF, they just won’t have any signatures.
• The digitally signed title page and committee signature pages should be in one PDF, separate from the thesis document. This avoids a DocuSign tag at the top of each page of the full thesis. Please use the following naming convention: authorLastName-kerb-degree-dept-year-sig.pdf (ex., montgomery-mssimon-phd-chemistry-2021-sig.pdf).
• Students should save their final thesis document as a PDF using the following file naming convention: authorLastName-kerb-degree-dept-year-thesis .pdf (ex., montgomery-mssimon-phd-chemistry-2021-thesis.pdf).
• Students should not deposit the PDF of their thesis via the Libraries Library’s voluntary submission portal.
• Please send an email to your advisor, Jennifer, and William which includes the final thesis document and file with the digitally signed title/committee signature pages with the following text:

Please also complete the MIT Doctoral Student Exit Survey and your Laboratory Safety Clearance Form .

Digital Signatures

Please see here for a full guide (with screenshots) to using DocuSign to obtain digital signatures

Required Signatures:

These should be everyone’s uploaded digital signatures in their own handwriting, not one of the pre-formatted signatures created by DocuSign.

• Your signature on the thesis title page
• Your advisor’s signature on both the title page and committee signature page
• Your thesis committee chair’s and member’s signatures on the committee signature page
• You do not need to have Adam Willard sign your title page, the Chemistry Education Office will take care of that
• Full thesis with no signatures (including unsigned title page and thesis committee signature page)
• Title page and committee signature page with signatures via DocuSign

Accessing DocuSign

Thesis Hold Requests

Details about requesting a thesis hold are available here and the requests are made to different offices based on the type of request. Please note that planned or pending submissions to scholarly journals related to thesis work will not be considered for thesis holds.

Written notification of patent holds and other restrictions must reach the MIT Libraries before the thesis in question is received by the MIT Libraries. Theses will not be available to the public prior to being published by the MIT Libraries. The Libraries may begin publishing theses in DSpace@MIT one month and one week from the last day of classes.

Graduate Student Exit Interviews

In order to best serve the educational, scientific, and social needs of graduate students in the Chemistry Department, it is critically important that Departmental leadership be appropriately informed of issues of importance to graduate students, ideally on an ongoing basis. Graduate student exit interviews provide information that alert the Department to acute issues that affect graduate students and provide data for longitudinal assessments of graduate student experience within the program.Graduate exit interviews are administered to all graduate students departing the Chemistry Department. The exit interview applies equally to graduate students departing with completed degrees (Ph.D. and M.S.) and without degrees.

• Graduating students will be sent a list of interview questions by the Chemistry Education Office when the student joins the degree list. Instructions about scheduling a time for the in-person or virtual discussion will be included with other informational correspondence from the Chemistry Education Office regarding degree completion. Graduating students will perform their exit interview after the thesis defense so as to avoid making the interview an additional burden.
• For students departing the program without a degree, the interview questions and instructions for scheduling an in-person discussion will be sent by the Chemistry Education Office at the point in time that a date for termination of their appointment in Chemistry is determined.
• For the majority of departing students, this interview coincides with the end of the semester, but a rolling schedule of surveys is anticipated.

Postdoctoral/Research Specialist Appointments

If you plan to transition to a postdoctoral/research specialist appointment within the Department of Chemistry at MIT, please contact Jennifer Weisman and  Chemistry HR as soon as possible. Your final signed thesis must be submitted before a postdoc appointment can start. If you are an international student, it is extremely important that you start this process early to allow sufficient timing for visa processing. In addition to talking with Jennifer and HR, please consult with the International Students Office .

Home > Sciences and Arts > Dept. of Chemistry > Dissertations and Master's Theses

Dept. of Chemistry Dissertations and Master's Theses

Explore our collection of dissertations and master's theses from the Department of Chemistry below.

Theses/Dissertations/Reports from 2023 2023

DETECTION AND MUTATIONAL ANALYSIS OF A HUMAN PROTEIN ASSOCIATED WITH CANCER AND CARDIOVASCULAR DISEASES , Priyanka Dipak Kadav

EXPLORING TURN-ON PROBES FOR GLUTs TARGETING AND ADVANCING SAFETY EDUCATION IN THE CHEMICAL SCIENCES: A TWO-PART DISSERTATION , Monica Mame Soma Nyansa

MULTILEVEL COMPUTATIONAL INVESTIGATION INTO THE CATALYTIC MECHANISMS OF MATRIX METALLOPROTEINASE-1 AND FAT MASS AND OBESITY-ASSOCIATED ENZYME , Ann Varghese

MULTISCALE MOLECULAR MODELING STUDIES OF THE DYNAMICS AND CATALYTIC MECHANISMS OF IRON(II)- AND ZINC(II)-DEPENDENT METALLOENZYMES , Sodiq O. Waheed

ORIGINS OF OPTICAL PROPERTIES IN NATURAL ORGANIC MATTER AND FLUORESCENT ANIMALS , Nastaran Khademimoshgenani

Small Molecules Targeting Fructose Transport , Nazar Gora

UHPLC/FT-MS NON-TARGETED SCREENING APPROACH FOR BIOMASS BURNING ORGANIC AEROSOL AND LIQUID SMOKE AS BIOMASS BURNING ORGANIC AEROSOL SURROGATE , D.M.R. Thusitha Dinusha Kumarihami Divisekara

Theses/Dissertations/Reports from 2022 2022

INTERFACIAL OXIDATION REACTIONS AND FILM NUCLEATION ON IRON SURFACES IN COMPLEX ENVIRONMENTS USING SPECTROSCOPY AT THE LIQUID/SOLID AND GAS/SOLID INTERFACE , Adambarage Chathura de Alwis

ISOLATION AND CHROMATOGRAPHIC SEPARATION OF CYTOTOXIC PLANT COMPOUNDS , Michael C. Hromada

ISOLATION, PURIFICATION, AND CHARACTERIZATION OF A NEW MANNOSE-BINDING PLANT LECTIN THAT RECOGNIZES FUNGAL ANTIGENS , Jessica C. Krycia

MULTILEVEL COMPUTATIONAL INVESTIGATION INTO THE DYNAMICS AND REACTION MECHANISMS OF NON-HEME IRON AND 2-OXOGLUTARATE DEPENDENT ENZYMES , Shobhit Sanjeev Chaturvedi

NON-CHROMATOGRAPHIC OLIGONUCLEOTIDE PURIFICATION AND AUTOMATED POLYETHYLENEGLYCOL SYNTHESIS , Dhananjani N. A. M. Eriyagama

STRUCTURAL AND FUNCTIONAL ANALYSIS OF A NEW CYTOLYSIN , Jared L. Edwards

SYNTHESIS AND DEVELOPMENT OF FLUORESCENT CARBON DOTS FOR SENSING AND BIOIMAGING APPLICATIONS , Parya Siahcheshm

Theses/Dissertations/Reports from 2021 2021

BASE-LABILE PROTECTING GROUPS FOR STEPWISE PEG SYNTHESIS , Logan D. Mikesell

COBALT, MOLYBDENUM, AND NICKEL COMPLEXES, NATURAL ZEOLITES, EPOXIDATION, AND FREE RADICAL REACTIONS , Nicholas K. Newberry

DESIGN AND DEVELOPMENT OF NEAR-INFRARED FLUORESCENT PROBES FOR SENSING pH, HYPOXIA AND PEROXYNITRITE , Shulin Wan

DETERMINATION OF MOLECULAR MARKERS OF VACCINIUM BERRY STANDARD REFERENCE MATERIALS THROUGH DIFFERENTIAL ANALYSIS WITH ULTRAHIGH RESOLUTION LC/MS , Abby Mikolitis

EXPLORING GLUT5 TARGETING FOR CANCER DIAGNOSIS AND THERAPY , Avik Ghosh

High-resolution molecular characterization of complex environmental mixtures: Aquatic dissolved organic matter and wildfire-influenced aerosol , Amna Ijaz

INVESTIGATING REDOX CHEMISTRY OF GRAPHITE, IRON OXIDE & IRON SURFACES , Mikhail Trought

Theses/Dissertations/Reports from 2020 2020

EXPLORING SUBSTRATE SPECIFICITY OF FRUCTOSE TRANSPORTERS EN ROUTE TO GLUT SPECIFIC PROBES FOR BIOCHEMICAL AND BIOMEDICAL APPLICATIONS , Vagarshak Vigenovich Begoyan

Macromolecular strategies for discovering disease-related proteins and new therapeutic agents , Christina Welch

RATIOMETRIC NEAR-INFRARED FLUORESCENT PROBES FOR THE SENSITIVE DETECTION OF INTRACELLULAR pH AND BIO-THIOLS IN LIVE CELLS , Shuai Xia

Theses/Dissertations/Reports from 2019 2019

Characterizing the physicochemical properties of TDP-43 protein and Acetylated Amyloid β peptides to discern its role in neurodegenerative diseases , Rashmi Adhikari

EXTREME MOLECULAR DIVERSITY IN BIOMASS BURNING ATMOSPHERIC ORGANIC AEROSOL OBSERVED THROUGH ULTRAHIGH RESOLUTION MASS SPECTROMETRY , Matthew Brege

METHOD CONSIDERATIONS FOR COMPOUND IDENTIFICATION IN COMPLEX MIXTURES USING ELECTROSPRAY IONIZATION ULTRAHIGH RESOLUTION MASS SPECTROMETRY , Tyler Leverton

MOLECULAR CHARACTERIZATION OF FREE TROPOSPHERIC ORGANIC AEROSOL AND THE DEVELOPMENT OF COMPUTATIONAL TOOLS FOR MOLECULAR FORMULA ASSIGNMENT , Simeon Schum

NEAR-INFRARED FLUORESCENT PROBES FOR SENSITIVE DETERMINATION OF LYSOSOMAL & MITOCHONDRIAL pH IN LIVE CELLS , Wafa Mazi

SMALL MOLECULE-BASED FLUORESCENT MOLECULAR PROBES FOR FACILITATING BIOMEDICAL RESEARCH: RATIONAL DESIGN AND BIOIMAGING APPLICATIONS , Xin Yan

Synthesis of Oligodeoxynucleotides Containing Sensitive Electrophiles , Shahien Shahsavari

TOWARDS THE DISCOVERY OF OLIGONUCLEOTIDE CROSS-LINKING AGENTS , Bhaskar Halami

Theses/Dissertations/Reports from 2018 2018

DEVELOPING NOVEL MOLECULAR IMAGING AGENTS FOR SHEDDING LIGHT ON OXIDATIVE STRESS , Shanshan Hou

DEVELOPMENT OF NEAR-INFRARED FLUORESCENT PROBES FOR MONITORING LYSOSOMAL pH CHANGES , Jianheng Bi

DIRECT MEASUREMENT OF RUPTURE FORCE OF SINGLE TRIAZOLE MOLECULE BY ATOMIC FORCE MICROSCOPE AND SOLID PHASE SYNTHESIS OF MONODISPERSE POLYETHYLENE GLYCOLS , Ashok Khanal

NOVEL FLUORESCENT PROBES FOR VISUALIZATION OF pH CHANGES AND Zn (Ⅱ) IONS IN LIVE CELLS , Mingxi Fang

PHYSICOCHEMICAL, SPECTROSCOPIC PROPERTIES, AND DIFFUSION MECHANISMS OF SMALL HYDROCARBON MOLECULES IN MOF-74-MG/ZN: A QUANTUM CHEMICAL INVESTIGATION , Gemechis Degaga

Theses/Dissertations/Reports from 2017 2017

DEVELOPMENT OF A SYSTEM TO STUDY THE EFFECTS OF HISTONE MUTATIONS AND POST-TRANSLATIONAL MODIFICATIONS ON NUCLEOSOME STRUCTURE VIA ATOMIC FORCE MICROSCOPY , Chelsea Nikula

Fluorescent Probe Development for Fructose Specific Transporters in Cancer , Joseph Fedie

GLYCOBIOLOGICAL STUDIES THAT CAN HELP THYROID CANCER DETECTION AND THERAPY , Ni Fan

Heterologous Expression and Purification of Full-Length Human Polybromo-1 Protein , Sarah Hopson

NOVEL BIOCOMPOSITES AND NANOFIBERS BASED ON MODIFIED BIOMASS MATERIALS TO FACILITATE GREENER APPLICATIONS , Soha Albukhari

Theses/Dissertations/Reports from 2016 2016

Effect of disulfide bond scrambling on protein stability, aggregation, and cytotoxicity , Colina Dutta

FORMATION AND DEACTIVATION OF TRIMETHYLALUMINUM IN AIR CONDITIONER SIMULATOR AND MCM-41 SUPPORTED SILVER NANOPARTICLES FOR OXIDATION OF OLEFINS , Zhichao Chen

NEAR-INFRARED WATER-SOLUBLE FLUORESCENT PROBES FOR THE DETECTION OF LYSOSOMAL pH AND Zn (II) IONS , Cong Li

Novel Carbohydrate-Dependent Biological Properties of Human Health Related Lectins and Glycoconjugates , Melanie Talaga

SENSING AND MAPPING OF SURFACE HYDROPHOBICITY OF PROTEINS BY FLUORESCENT PROBES , Nethaniah Dorh

THE EFFECT OF POSTTRANSLATIONAL MODIFICATIONS ON PROTEIN AGGREGATION, MORPHOLOGY, AND TOXICITY , Mu Yang

Reports/Theses/Dissertations from 2015 2015

BIOLOGICAL MATERIALS: PART A. TEMPERATURE-RESPONSIVE POLYMERS AND DRUG DELIVERY AND PART B. POLYMER MODIFICATION OF FISH SCALE AND THEIR NANO-MECHANICAL PROPERTIES , Xu Xiang

DESIGN AND DEVELOPMENT OF BODIPY-BASED FLUORESCENT PROBES FOR SENSING AND IMAGING OF CYANIDE, Zn (II) IONS, LYSOSOMAL pH AND CANCER CELLS , Jingtuo Zhang

Extracellular expression of alkaline phytase in Pichia pastoris and Development of Nuclear Magnetic Resonance spectroscopy methods for structural investigation of inositol polyphosphates , Sasha Teymorian

ON THE PROTECTIVE PROPERTIES OF GLYCINE BASED OSMOLYTES IN A THIOL REDUCING ENVIRONMENT , John Michael Hausman

SYNTHETIC OLIGODEOXYNUCLEOTIDE PURIFICATION VIA CATCHING BY POLYMERIZATION , Suntara Fueangfung

Reports/Theses/Dissertations from 2014 2014

DESIGN, SYNTHESIS AND APPLICATIONS OF FLUORESCENT AND ELECTROCHEMICAL PROBES , Giri K. Vegesna

EVOLUTION OF SELECTED ISOPRENE OXIDATION PRODUCTS IN DARK AQUEOUS AMMONIUM SULFATE , D.M. Ashraf Ul Habib

MOLECULAR CHARACTERIZATION OF ATMOSPHERIC ORGANIC MATTER IN BIOGENIC SECONDARY ORGANIC AEROSOL, AMBIENT AEROSOL AND CLOUDS , Yunzhu Zhao

NON-CHROMATOGRAPHIC PURIFICATION OF SYNTHETIC BIO-OLIGOMERS , Durga Prasad Pokharel

PURIFICATION AND CARBOHYDRATE BINDING PROPERTIES OF TWO NEW PLANT PROTEINS , Robert K. Brown

Reports/Theses/Dissertations from 2013 2013

ACETYL RADICAL IN TOBACCO SMOKE: DETECTION, QUANTIFICATION AND SIMULATION , Na Hu

CHARACTERIZATION OF TWO NOVEL MONOCOT MANNOSE BINDING LECTINS PURIFIED BY ‘CAPTURE AND RELEASE’ METHOD , Ashli L. Fueri

Development and characterization of fluorescent pH sensors based on porous silica and hydrogel support matrices , Qili Hu

Enhancement of heterologous expression of alkaline phytase in Pichia pastors , Mimi Yang

Modern Computational Chemistry Methods for Prediction of Ground- and Excited-State Properties in Open-Shell Systems , Nina Tyminska

Oligodeoxynucleotide synthesis using protecting groups and a linker cleavable under non-nucleophilic conditions , Xi Lin

STUDIES OF FUNCTIONALIZED NANOPARTICLES FOR SMART SELF-ASSEMBLY AND AS CONTROLLED DRUG DELIVERY , Xiaochu Ding

THERMORESPONSIVE PROPERTIES OF GOLD HYBRID NANOPARTICLES OF POLY(DI(ETHYLENE GLYCOL) METHYL ETHER METHACRYLATE) (PDEGMA) AND ITS BLOCK COPOLYMERS WITH DIFFERENT ANCHORING REGIMES , Martha Juliana Barajas Meneses

TUNING FLUORESCENT PROBES FOR BIOMEDICAL APPLICATIONS , Nazmiye Bihter Yapici

Reports/Theses/Dissertations from 2012 2012

Biological materials : Part A. tuning LCST of raft copolymers and gold/copolymer hybrid nanoparticles and Part B. biobased nanomaterials , Ning Chen

Characterization of water-soluble organic compounds in ambient aerosol using ultrahigh-resolution elctrospray ionization fourier transform ion cyclotron resonance mass spectrometry. , Parichehr Saranjampour

COORDINATION CHEMISTRY OF BIS(BENZYL)PHOSPHINATE , John S. Maass

DESIGN AND SYNTHESIS OF NOVEL SYNTHETIC ANTIOXIDANTS FOR THE TREATMENT OF OXIDATIVE STRESS RELATED DISEASES , Srinivas Rao Mandalapu

Indole based antioxidants for the treatment of ischemia reperfusion injury , Andrew Chapp

Performance evaluation and characterization of symmetric capacitors with carbon black, and asymmetric capacitors using a carbon foam supported nickel electrode , JinJin Wang

Soft Lewis acid catalyzed cycloisomerization of oxo-alkynes and enynes , Zezhou Wang

Reports/Theses/Dissertations from 2011 2011

Multimetallic complexes based on phosphine- and phosphine oxide- appended p -hydroquinones , Louis R. Pignotti

Performance evaluation of a novel asymmetric capacitor using a light-weight, carbon foam supported nickel electrode , Padmanaban Sasthan Kuttipillai

Structural characterization of water-soluble atmospheric organic matter by ultrahigh-resolution mass spectrometry , Jeffrey P. LeClair

Syntheses and structures of molybdenum and tungsten complexes capable of epoxidaton and copper coordination polymers and dendrimers , Linsheng Feng

Synthesis of chiral ferrosalen ligands and their applications in asymmetric catalysis , Xiang Zhang

Reports/Theses/Dissertations from 2010 2010

Syntheses and characterization of monomeric Mo(VI) complexes with bidentate phosphine oxide ligands and dimeric and tetrameric Mo(V) clusters with benzoic acid and phosphinic acid derivatives, containing MoO 2 , Mo 2 O 2 ( μ -O) 2 and Mo 4 O 4 ( μ 3 -O) 4 , Soumyashree Sreehari

Reports/Theses/Dissertations from 2009 2009

Molecular interaction between perthiolated [beta]-cyclodextrin (CD) and the guests molecules adamantaneacetic acid (AD) and ferroceneacetic acid (FC); and the effect of the interaction on the electron transition of CD anchored particles , Ming Ning

Reports/Theses/Dissertations from 2005 2005

Sulfoxides as an intramolecular sulfenylating agent for indoles and diverse applications of the sulfide-sulfoxide redox cycle in organic chemistry , Parag V. Jog

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A guide to writing up your chemical science thesis

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This guide aims to give you guidance on how to write your thesis so that your research is showcased at its best. It includes suggestions on how to prepare for writing up and things to consider during the final stages. 

• Higher-order thinking and metacognition
• Investigation
• Manipulating data
• Working independently
• Communication skills

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How to write a PhD thesis

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Five tips for communicating your research

Writing a thesis is an inevitable part of a chemistry PhD. Yet it can be a daunting task. While everyone’s personal circumstances vary – university rules, the chemistry discipline and supervisor relationships – the most difficult part is actually starting to write. Adam Clancy of University College London, UK; Chiara Giorio of the University of Cambridge, UK; and I (a recent PhD graduate) reflect on our experiences to offer some advice and tips.

Start writing early

Ideally, if you receive funding you want to finish before the money stops coming in. ‘It’s such an appealing thing to think one more experiment will pull everything together,’ says Clancy. ‘It’s better to just draw a line in the sand in advance.’ This was a goal I set myself, and it proved to be a catalyst to my productivity. Clancy’s experience was different: ‘I got a postdoc and then wrote in the evenings, which was a terrible, terrible idea.’ Sometimes though, a promising job offer or unforeseeable circumstances means this is your only option for completion. Whatever your circumstances, Giorio advises ‘to write as much as you can, every day,’ even if it’s just experimental procedures or summaries.

For me, getting started was the hardest part. Thinking of a thesis as a series of small, manageable chapters rather than a whole book helped me compartmentalise. Once you start writing, you build up momentum. Having something that you can look back at as a starting point is better than staring at a blank page.

Make a plan

Devise a workplan with your supervisor before you start writing. ‘It should be a discussion with them about where they think the good results are – how you can split up all your work into manageable, multiple sections,’ explains Clancy. Spend time ‘understanding what are the key messages that you want to get across,’ says Griorio. During writing, send chapters to your supervisor for revision and go over them together. ‘The first draft doesn’t need to be perfect’ – and it won’t be – but this will give you a better idea of what your supervisor expects. ‘The first time you write something, it’s very difficult,’ Griorio explains, so it’s good to solicit feedback early on. But it’s not just your supervisor you can ask – peers, friends and family can contribute ‘even if only catching typos’, she adds.

No need to work sequentially

Start with the chapter you’re most comfortable working on – you don’t need to write the thesis in order. I found switching between chapters helped. Some days I had brain fog when writing up my results so I would work on the literature review and come back to writing up the results when I had the mental capacity. The structure of the thesis also does not have to be chronological: Clancy used what he did towards the end of his PhD to form his first results chapter. ‘You’re not recounting what you did for three years,’ he explains. ‘It shouldn’t be a biography of your research.’

Figures are your friends

Images can reveal a lot about your work. ‘I’m a fan of basically never really needing words,’ reveals Clancy. ‘It’s worth taking the time to make your graphs look highly presentable and really clear.’ Graphs and images are not only useful in breaking up large bodies of text, but they also provide context and meaningful data for your discussion. ‘You can start with just putting some figures together and some bullet points,’ says Giorio, noting that graphs assist with the initial hurdle of getting something written down. Clancy suggests you ‘go to the papers you like and see how they present data and be inspired by that’. Don’t take shortcuts with figures – a lesson I learned. I had to do corrections on my graphs after my viva that could have easily been avoided if I had been more diligent when producing the figures in the first place.

Don’t worry

You are an expert in your research so be confident about your writing. ‘If you’ve got to this point, you’re probably good enough to pass a PhD,’ Clancy says. You have put in years of work and all you must do now is communicate it. But don’t let writing consume your life – take regular breaks, keep active and balance your time with hobbies and friends. By taking care of your physical and mental health, you will be in a better position to deliver your best work.

I found the writing process unexpectedly fun and therapeutic. There were days when nothing would come to me, but I would say ‘tomorrow is a new day’. Try not to put too much pressure on yourself. At the end of it, you will hopefully look at your thesis with pride and a sense of accomplishment.

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Edinburgh Research Archive

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Chemistry thesis and dissertation collection

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The School of Chemistry at the University of Edinburgh is the top rated for teaching and research in Scotland.

Presented here is a selection of research from the School

This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.

Recent Submissions

Probing the organisation and turnover of synaptic proteins at the nanometre length scale , molecular dynamics simulations of engine lubricant additives , utilising non-canonical amino acids in the design of artificial enzymes: an exploration of cu-enzymes, steroid carrier protein scaffolds and synthetic biology , magnetism of multinuclear 3-d transition metal complexes of 2-hydroxymethylpyridine , antimicrobial polymers , biological control of crystallization by marine phytoplankton to produce functional mineral structures , low-temperature phase-change materials for energy-storage applications , biocompatible aldehyde modification in escherichia coli , novel smart probes for detection of neutrophil activation and net formation and investigation of etosis in fish erythrocytes , improving rapid pathogen detection: towards a gram-selective lateral flow test , towards predicting and tailoring properties of energetic materials , development of liquid crystal lasers for application in fluorescence microscopy , block by block: developments in nmr methodology , development and understanding of iron-catalysed c–h functionalisation reactions , developing new processes for the solvent extraction of precious metals , effect of drainage and drain-blocking on the molecular and microbial composition of blanket bog peat , investigating the biomedical applications of coordination cages , gas phase electronic spectroscopy of ionic carbon chains, rings, fullerenes and analogues , novel synthetically accessible polymers of intrinsic microporosity (pims) , fluorescence properties of nucleobase analogues in dna under one- and two-photon excitation .

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DOCTORAL THESES (chemistry) Collection home page

• 2 Hussen, Abdulkadir Shube
• 2 Kumar, Neeraj
• 2 Kumar, Rajeev
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• 2 Sharma, Rashmi
• 2 Singh, Pallavi
• 2 Singh, Rashmi
• 1 AbdulKadir, H. K.
• 1 Abdullah, Adil Ali
• 348 CHEMISTRY
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• 129 2010 - 2020
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• 18 Mahesh, V. K.
• 18 Singh, A. K.
• 17 Sharma, C. L.
• 16 Tandon, S. N.

Chemistry Theses

Permanent uri for this collection.

This collection is made up of doctoral and master theses by research, which have been received in accordance with university regulations.

For more information, please visit the UCD Library Theses Information guide .

Recent Submissions

• Publication Superparamagnetic Nanoparticles for the Assessment of Intracellular Nanoparticle-Cell Interactions ( University College Dublin. School of Chemistry, 2022 ) Cursi, Lorenzo   ; 0000-0003-4505-1218 Since their discovery, nanomaterials have been employed in an increasing number of products and applications. Thanks to their unique properties they enabled the advancement of many technologies and improved our lives under several aspects. Because of their nanometric dimensions, nanomaterials interact with the biological matter in a completely different way compared to their smaller (molecular scale) or larger (macro scale) counterparts. Despite the efforts of the scientific community in unravelling the network of machineries involved in the interaction of nanomaterials with the cells and human body, our understanding of the bio-nano interactions is still limited. The lack of knowledge around the dynamics that regulate the nanoparticles’ (NPs) trafficking in the human body is limiting the development of nanomedicine and, at the same time, is rising concerns in the regulatory bodies for the safe commercialisation of nanomaterial-based products. One of the main issues related to this critical gap in the knowledge is the lack of methodologies and tools that prevents unravelling the complexity of the bio-nano interactions. Techniques commonly used for the study of the intracellular dynamics result limiting for the study of the NPs intracellular trafficking for which the combination of different analysis and methodologies is required to obtain reliable and robust results. However, the correlation of data from different techniques is difficult when different NPs systems are used for the experiments. In this thesis, we develop new tools and methodologies for the study of the bio-nano interactions, exploiting one of the unique properties of iron oxide NPs, the superparamagnetism. In this context, superparamagnetic NPs are extremely useful tools because allow to label the machineries involved in the intracellular trafficking of NPs and enable their isolation from the biological matrix, which in order allows a more in-depth downstream analysis. To label the machineries involved in the intracellular trafficking with superparamagnetic NPs, two strategies are possible: exploiting the natural uptaking mechanisms of the cells or targeting specific compartments with NPs designed ad hoc. To exploit the first strategy, we designed multifunctional core-shell NPs with iron oxide multicores that provided the superparamagnetic properties and a silica shell doped with an organic fluorophore. Combining the magnetic and fluorescent properties in one nanoconstruct enabled to resolve the NPs intracellular trafficking by optical microscopy and to isolate the vesicles loaded with the NPs by magnetic separation, at different stages of their voyage inside the cell. The vesicles were then analysed with a set of technique to evaluate their integrity and functionality. To exploit the second strategy, we designed antibody grafted iron oxide NPs for the targeting of specific biological species. For this purpose, we adopted a thoughtful strategy of NPs surface modification that enabled the grafting of the antibody through bio-orthogonal chemistries, stabilise the particles in biological conditions, and limit the adsorption of undesired biomolecules typically responsible for NPs off-targeting. Although this second nanoconstruct is still under development, the preliminary results showed excellent targeting ability and specificity. Overall, the work presented in this thesis provides a solid base for the isolation, by magnetic separation, of biological species involved in the NPs intracellular trafficking and for the development of methodologies for the investigation of the machineries involved in the process.   12
• Publication The Physiochemical and Biological Characterization of Nanostructured Materials Derived from Natural Processes ( University College Dublin. School of Chemistry, 2022 ) Petseva, Vanya   ; 0000-0002-7013-0535 The thesis focuses on the study of nanostructured materials obtained from natural sources. The work presented in this thesis was designed to 1) develop protocols for a complete Physico-chemical characterization of micro-and nanomaterials derived from calcified seaweed. Such protocols were achieved by combining several different characterization techniques and were able to unravel unexpected material features at the nanoscale; 2) obtain nanostructured metallic particles from the calcified seaweeds through a multistep extraction protocol and investigate their interactions with cells. The extensive characterization work carried out along this project, especially using electron microscopy, also allowed to develop methods for the visualization of endogenous biological material associated with nanoparticles after their interaction with biomolecules and the intracellular environment.   111
• Publication Complex Nanostructures and Bio-Nanoscale Interactions: Well Defined Synthesis, Identification and Biological Effects ( University College Dublin. School of Chemistry, 2022 ) Zhang, Wei   In this thesis, a framework was proposed in chapter II, aiming to identify distinct shape populations and build a quantitative linkage of well-defined nanoscale shapes to biological impacts. This inductive nanoscale shape discovery and evaluation framework is biologically relevant, and we believe by utilizing machine learning it could benefit the field of shape dependent therapy. In chapter III, the shape dependent histone modifications were reported. As histone modifications are one of the crucial epigenetic regulators that control chromatin structure and gene transcription, shape dependent histone modifications indicate that some important cellular phenotypes differences induced by nanoscale shapes may be related to the histone modifications, which opens a new window for the investigation of nanoscale shape effects and nano therapy. In chapter IV, we proposed a method to modify the surface of the nanostructures by endogenous cellular processes and studies found that this re-engineered particle complex was able to transfer the loading genes to recipient cells, which indicates their potential to work as an efficient nucleic acid delivery machine.   5
• Publication Investigation of Nanostructures generated in cells ( University College Dublin. School of Chemistry, 2022 ) Lawless, Alexandria   ; 0000-0003-1560-9823 Nanoparticles have established themselves firmly within the biomedical field due to their fine tuneability. Recent work explores NP behaviour in complex biological media lending itself to a growing body of research investigating the biological identity of NPs. Biomolecules have been found to readily adsorb to NPs upon interaction in complex biological media forming a protein shell. Previously viewed as an impediment to NP application in vivo, the protein shell, now referred to as the ‘biological corona’ displays potential for beneficial and independent applications. This has highlighted the need for a sounder understanding of the way in which cells receive, process, and clear nanoparticles and the pathways implicated. This research investigates the ability of magnetic magnetite multicore silica fluorescent nanoparticles to adsorb biomolecules to form a biological corona and further enrich with target EGFP fusion proteins upon administration to and interaction with stable EGFP-transfected, adherent cells in culture. The cell – engineered, biosynthetic particle recovered following internalisation, trafficking and subsequent recycling will be referred to here as a bio nanostructure (BNS). This research builds upon a large body of data encompassing all proteins comprising the BNS generated in HEK-293T cells. Here I will explore several highly abundant RNA binding proteins that are incorporated onto the BNS during cellular processing of the nanoparticle-protein corona. The application of high-resolution confocal laser scanning microscopy, along with a ‘masking’ technique will facilitate observation of EGFP fusion proteins on the BNS coat. The results presented herein support the establishment of a reliable and reproducible method for the fluorescent mapping proteins of interest on cell – generated bio nanostructures. It provides a platform for further investigation of potential subpopulations of cell generated bio nanostructures and the intricate processing networks underlying the export of these bio nanostructures.   18
• Publication The Preparation and Application of Novel Planar Chiral Ferrocenyl Ligands in Asymmetric Catalysis ( University College Dublin. School of Chemistry, 2022 ) Benson, Annette   ; 0000-0002-7249-5271 Asymmetric catalysis, employing both transition-metal complexes of chiral ligands and organocatalysts has become one of the most popular methods for the preparation of enantioenriched and enantiopure compounds. This is important for the synthesis of chiral biologically active compounds or drug targets. The design of efficient and novel chiral ligands and catalysts has become a prominent area of chemistry in itself. In this PhD thesis, the concept of chirality and the importance of chiral synthesis in chemistry is introduced while highlighting the interesting properties of ferrocene and the development of chiral ferrocenyl scaffolds in this expanding area of chiral ligand synthesis. The aim of this project was to exploit the reactivity and selectivity of ferrocenyl mono- and diketone scaffolds optimised previously in the group to develop a range of interesting chiral catalysts and ligands. The first of these novel structures was an extended diol structure which would serve as a second generation to diols produced previously in the group which possessed a quaternary centre at the alpha-ferrocenyl position. Three chiral diols extended by two methylene units, were synthesised in six high yielding steps with minimum purification required. These catalysts were applied in an asymmetric hetero Diels-Alder reaction affording the product in low yield and low enantioselectivity of up to 33% ee. The presence of a tertiary stereocentre at the alpha-ferrocenyl position caused instability issues compared to the previous library. Following on from this, five novel ferrocenyl aniline-containing amino alcohol ligands were developed diastereoselectively in as few as three high yielding steps. These ligands were very successful in asymmetric diethylzinc addition to aldehydes, achieving ees of up to 99% and in asymmetric phenyl transfer reactions with moderate yields and enantioselectivities of up to 88%. With the assistance of X-ray crystallographic studies, transition states for the novel gamma-amino-alcohol system were proposed to explain the stereochemical outcome of the reactions. Finally, a fascinating rearrangement was observed when attempting to synthesise a ferrocenyl phosphoramidite, resulting in the formation of novel chiral phosphonamidate structures. Compounds that possess this moiety have been shown to evoke therapeutic effects such as anti-cancer and anti-viral properties. By utilising both X-ray crystallography and 31P NMR spectroscopy, a mechanistic understanding of phosphonamidate formation was reached, with four diastereomers theoretically possible in their synthesis. By employing a series of secondary amines, six chiral phosphonamidate analogues were synthesised with both a major and minor diastereomers isolated and their structures successfully elucidated.   8
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Dissertations-Theses

Dissertations and theses.

Every graduate student has to write a thesis or dissertation before being awarded a MS or Ph.D degree. Browse abstracts and in some cases the complete text of some of our previous students work on the ETD website .

View a complete list of Ph.D degrees awarded by the chemistry department since 1913.

ETD Submission Process

All theses and dissertations are submitted online. Visit the ETD Website for more information on the process.

Public Presentations

View our events section to find upcoming public presentations by graduate students at the Chemistry department.

Reserve a Room

All students seeking to arrange a room and the publicity for the public portion of their comprehensive defense (if required), thesis (MS) defense, or dissertation (PhD) defense should reserve a room no less than one month in advance of the defense date.

Please contact Mary Beth at [email protected] to make the room reservations.  Please contact her with any questions regarding the room reservation process.