Master's Thesis

2D Metal-Organic Frameworks Featuring Threefold-Coordinated Metal Centres

Final Thesis 11.96 MB

Author of thesis: Ing. Alexandr Cohl

Acad. year: 2025/2026

Supervisor: Dr. techn. Zdeněk Jakub

Reviewer: Ing. Dr.techn. Jiří Pavelec

Abstract:

This master's thesis focuses on the preparation and subsequent characterization of two-dimensional metal-organic frameworks (2D MOFs) with threefold coordinated metal centers on the surfaces of Au(111) monocrystals and graphene. These frameworks were prepared using on-surface synthesis method consisting of deposition of organic ligands and metal atoms under ultra-high vacuum (UHV) conditions. The structure and electronic properties of the resulting layers were characterized using scanning tunneling microscopy (STM) and low-energy electron microscopy (LEEM).

The experimental section describes the synthesis of the FeHHTP system on the surface of Au(111) and its subsequent analysis, primarily with regard to structural arrangement. The work also investigates the FePBP system, for which density functional theory (DFT) calculations were used to study the stability, reactivity, and electronic properties of its metal centers. The final part of the thesis focuses on three distinct structural phases of the NiDCA system on graphene and investigates the effect of oxygen intercalation on the structure of each phase and their thermal stability.

Keywords:

metal-organic frameworks, threefold coordination, on-surface synthesis, ultra-high vacuum, scanning tunneling microscopy, low-energy electron microscopy, graphene, density functional theory, intercalation, structural analysis, thermal stability

Date of defence

16.06.2026

Result of the defence

Defended (thesis was successfully defended)

znamkaAznamka

Grading

A

Process of defence

Po otázkách oponenta bylo dále diskutováno: Způsob měření úhlů a nejistoty měření jejich hodnot. Student na otázky odpověděl.

Language of thesis

English

Faculty

Department

Study programme

Physical Engineering and Nanotechnology (N-FIN-P)

Composition of Committee

prof. RNDr. Tomáš Šikola, CSc. (předseda)
prof. RNDr. Jiří Spousta, Ph.D. (místopředseda)
prof. RNDr. Pavel Zemánek, Ph.D. (člen)
prof. Mgr. Dominik Munzar, Dr. (člen)
doc. Mgr. Adam Dubroka, Ph.D. (člen)
prof. Ing. Jan Čechal, Ph.D. (člen)
prof. RNDr. Jiří Petráček, Dr. (člen)
prof. RNDr. Radim Chmelík, Ph.D. (člen)
doc. Ing. Radek Kalousek, Ph.D. (člen)
prof. Ing. Miroslav Kolíbal, Ph.D. (člen)
doc. Ing. Stanislav Průša, Ph.D. (člen)
doc. Mgr. Vlastimil Křápek, Ph.D. (člen)
RNDr. Antonín Fejfar, CSc. (člen)

Supervisor’s report
Dr. techn. Zdeněk Jakub

Student Alexandr Cohl se ve své diplomové práce věnoval problematice on-surface syntézy 2D metalo-organických sítí obsahujících kovové atomy ve třívazné koordinační geometrii. Teoretická část obsahuje úvod do tématu a popisuje parametry definující strukturu 2D metal-organických sítí na površích, hlavní důraz je kladen na parametry umožňující stabilizovat kovové atomy ve třívazné geometrii. Součástí teoretické části je popis použitých experimentálních a výpočetních metod. Následující experimetální část se pak věnuje třem zkoumaným metalo-organickým systémům: Fe-HHTP, Fe-PBP a Ni-DCA. Každý z těchto systémů byl zkoumán jinou metodou: Fe-HHTP byl měřen pomocí nízkoteplotního STM/STS, Fe-PBP byl zkoumán výpočetními metodami DFT, a Ni-DCA byl analyzován primárně metodou LEEM/LEED v kombinaci s STM.

Student se svých úkolů zhostil aktivně a zodpovědně. Téma bylo komplikované několika experimentálními zádrhely - hlavně kontaminací dodaných PBP molekul a problémy s reprodukovatelností depozičních parametrů DCA. Přes tyto nesnáze student prokázal, že je schopen úspěšně zvládnout zvolené experimentální a výpočetní metody, a výsledky správně interpretovat. Naměřená a vypočtená data jsou pro výzkumnou skupinu cenná, a s velkou pravděpodobností budou součástí plánovaných publikací.

Samotná práce je psána čtivě, na vysoké jazykové úrovni, je doplněna mnoha obrázky, a odkazy na relevantní literaturu. Menší výtky lze najít: interpretace Ni-DCA kapitoly může být pro nezasvěcené čtenáře hůře pochopitelná, a některé odkazů na literaturu by šlo vysvětlit lépe. To jsou ale jen malé chybky na jinak výborné práci. Celkově oceňuji studentovu schopnost rychlé orientace v nových tématech, samostatnost a efektivitu. Stanovené cíle diplomové práce považuji za splněné a práci doporučuji k obhajobě s navrhovaným hodnocením A.
Evaluation criteria Grade
Fulfilment of requirements and objectives of assignment A
Working process, extent and suitability of applied methods A
Scholarly contribution and originality A
Ability to interpret achieved results and draw conclusions A
Applicability of results in practice or theory A
Logical arrangement of thesis and its layout A
Grafic layout, used style and language level B
Work with used sources including quotations B
Student's independence when working on the topic A

Grade proposed by supervisor: A

Reviewer’s report
Ing. Dr.techn. Jiří Pavelec

This timely and demanding master’s thesis is motivated by the field of single-atom catalysis. It focuses on the preparation and characterization of chemically reactive two-dimensional metal-organic frameworks (MOFs) featuring threefold-coordinated metal centers. The work effectively spans three main investigative pillars: the experimental synthesis of FeHHTP on Au(111); a first-principles modeling and density functional theory (DFT) study of FePBP on graphene; and the investigation of NiDCA phases on both pristine and oxygen-intercalated graphene.

A key strength of this work is the student's proactive problem-solving and adaptability. When precursor contamination prevented the planned FePBP experiments, the student did not abandon this section but instead developed it into a meaningful DFT study. If expanded, this computational work alone could form the baseline for an independent master's thesis. Successfully combining experimental ultra-high vacuum (UHV) surface-science skills with computational insights demonstrates a highly valuable, interdisciplinary skillset. Furthermore, the thesis is very well-connected to existing literature and prior research in the field.

Only minor shortcomings are observed. Primarily, key experimental parameters, specifically the temperatures used for STM imaging and STS, are placed in general methodology sections rather than directly alongside the presented data. Additionally, the presentation would benefit from listing specific preparation conditions directly within the key figure captions for easier reading.

Despite these minor limitations, the student convincingly demonstrates the ability to acquire and analyze complex experimental data while performing first-principles calculations. Overall, all assigned objectives were successfully fulfilled, and the work fully meets the requirements for a master's thesis. The primary goal of this work, growing chemically reactive 2D MOFs, is an inherently difficult task, as chemical reactivity and structural stability naturally work against each other. Therefore, the partial but clear success achieved here represents a significant step toward utilizing these 2D MOFs as well-defined single-atom model catalysts, successfully bridging the gap to the reactivity required in real-world catalysis.
Evaluation criteria Grade
Fulfilment of requirements and objectives of assignment A
Working process, extent and suitability of applied methods A
Scholarly contribution and originality A
Ability to interpret achieved results and draw conclusions A
Applicability of results in practice or theory A
Logical arrangement of thesis and its layout A
Grafic layout, used style and language level A
Work with used sources including quotations A
Topics for thesis defence:
  1. How were the e-beam evaporation rates for the metals calibrated? What is the standard calibration tool for this process, and what is its working principle?
  2. For the FeHHTP/Au(111) system, annealing at 300 °C forms the MOF-like phase, while 325 °C reduces coverage. Could a lower-temperature or stepwise annealing approach optimize the 2D MOF coverage? Additionally, which in situ spectroscopic or microscopic methods could help optimize these growth parameters?
  3. What is the methodology for comparing reciprocal-space LEED patterns with real-space measurements from STM images?
  4. Why was CO selected as probe molecule for testing FePBP reactivity? What other probe molecules would be interesting to explore?
  5. If unrestricted access to any experimental technique or facility worldwide were available, what would be the ideal "dream experiment" to advance this research?

Grade proposed by reviewer: A

Responsibility: Mgr. et Mgr. Hana Odstrčilová