Theoretical Study on Formation and Reactivity of Coordination Compounds Employing AFIR [an abstract of entire text]

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Theoretical Study on Formation and Reactivity of Coordination Compounds Employing AFIR [an abstract of entire
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Skjelstad, Bastian Bjerkem

北海道大学. 博士(総合化学) 甲第15387号

2023-03-23

http://hdl.handle.net/2115/91271

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theses (doctoral - abstract of entire text)

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学 位 論 文 の 要 約

博士の専攻分野の名称 博士（総合化学）

氏名 シェルスター バスティアン ビェルケム

学 位 論 文 題 名

Theoretical Study on Formation and Reactivity of Coordination Compounds Employing AFIR
（人工力誘起反応法を用いた配位化合物の生成と反応性に関する理論的研究）
Coordination compounds have emerged as an intriguing class of functional materials due to their desirable
properties for a variety of applications, including gas storage and separation, catalysis, drug delivery and
biological imaging and sensing. In this Thesis, two different subclasses of coordination compounds, namely
metal-organic frameworks (MOFs) and transition metal (TM) complexes, are surveyed by means of quantum
chemical calculations to evaluate their early-stage self-assembly mechanisms and catalytic properties,
respectively.
Metal-Organic Framework Formation
Synthesis of new MOFs relies on chemical intuition and serendipity, as their mechanisms of formation are
poorly understood at present. As an attempt to bridge the gap, and enable targeted synthesis of MOFs with
desired properties, a general workflow based on the artificial force induced reaction (AFIR) method is devised
to analyze the formation of MOF units through automated reaction path exploration and kinetic simulations
enabling identification and analysis of the dominating pathways of assembly.
The developed workflow is applied to study the formation of the SIFSIX-3-Zn MOF node [Zn(pyz)4(SiF6)2]2- (pyz
= pyrazine), finding that assembly proceeds in a stepwise manner, in which the organic pyz ligands coordinate
to the inorganic core structure one at a time, while the coordination of the SiF6–Zn–SiF6 unit flexibly changes
to accommodate for the incoming organic ligands. Moreover, interconvertibility between reaction intermediates
and competing reaction pathways likely operating simultaneously are observed, providing a plausible
explanation for stochastic processes believed to be key in MOF formation.

A similar workflow is used to investigate formation of paddlewheel structures, one of the most common
motifs in MOFs, finding that axially coordinating ligands play a crucial role in stabilizing reaction
intermediates as well as the assembled structures. In Zn-based paddlewheels, assembly is facilitated by
axially coordinating ligands, which stabilize the paddlewheel structure. Cu-based structures, on the other
hand, depend to a lesser extent on the stabilization by axial ligands, implying that open metal site
formation, of importance to catalysis and adsorption, is more accessible. Four structures, [Zn2(OAc)4]  2
H2O, [Zn2(OAc)4]  2 py, [Cu2(OAc)4] and [Cu2(OAc)4]  2 H2O (OAc = acetate, py = pyridine), are found to
form through a single phase directly from the reaction mixture, whereas [Cu2(OAc)4]  2 py forms via two

phases. Despite formation of [Cu2(OAc)4]  2 py through a single phase being thermodynamically
conceivable, as it is the global minimum of the AFIR calculation, it is kinetically inaccessible as
demonstrated by the kinetic simulation. Instead, [Cu2(OAc)4]  2 H2O must first be formed, and through
ligand exchange where H2O is replaced by py, [Cu2(OAc)4]  2 py is formed. This rationalizes the
experimental synthesis procedure, which is also performed in two steps.

Transition Metal Catalysis
Methane has the highest gravimetric energy density of all hydrocarbons, but its low density leads to a poor
volumetric energy density. Hydroxylation to methanol is a promising strategy to increase its density, of
interest to chemical industry, however no 3d TM catalyst capable of selectively oxidizing methane to
methanol is currently known. In this Thesis, the electronic and reactive properties of TM-doped cobalt–oxo
cubane complexes are studied, enabling design principles for the development of new methane
hydroxylation catalysts to be established.
The electronic properties of [M(O)Co3O4(OAc)4(py)3] (M = Cr, Mn, Fe, Mo, Tc, Ru, Rh) are studied, and based
on the high terminal oxyl spin density of the Fe-based cubane, it is proposed as a catalyst for alkane
hydroxylation and compared to the experimentally known Ru-doped cubane. Hydroxylation of methane is
found to be feasible for the Fe cubane, over a rate-determining H atom abstraction barrier of 24.6 kcal/mol.
AFIR calculations provide further evidence for the validity of the oxygen rebound mechanism for methane
hydroxylation as the operating lowest-energy mechanism for heterometallic oxo cubanes. ...

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