Piotr P. Romańczyk and Stefan S. Kurek describes the progress in efficient solvation models that helped to develop effective computational protocols allowing for
accurate reproduction of experimental redox potentials of mono- and dinuclear
complexes, including electrocatalytically relevant systems and mixed-valence
compounds. Examples of such computational protocols that use DFT combined
with continuum solvent models, as well as a mixed, discrete-continuum approach,
are shown in this contribution. The ferrocenium/ferrocene system, widely used as
an internal standard, is discussed, followed by the presentation of intriguing
properties of mono- and bimetallic Mo/W scorpionates, in particular electrochemical communication between metal centers and a baffling dehalogenation, the
mechanism of which was elucidated only owing to the application of DFT-D3
calculations.
The end section of the book entails four chapters and discusses enzymatic and
biomimetic systems. The topic is singled out even if problems intrinsic to very large
systems incorporating transition metals are generally common; nevertheless, transition metals in bio- or bioinorganic complexes share several specific properties and
specific techniques common among them but distinctive from inorganic transition
metal complexes. This part opens with Chapter “The Quest for Accurate
Theoretical Models of Metalloenzymes: An Aid to Experiment” by Matthew G.
Quesne and Sam P. de Visser. The chapter reviews two key computational
approaches to metalloenzymes, namely quantum mechanics/molecular mechanics
(QM/MM) on complete enzyme structures and QM cluster models on active site
structures only. The former take the structure of the full enzyme with a solvent layer
into consideration, whereas the latter only include key features of the first and
second coordination sphere. The examples are discussed where the QM cluster
approach worked well; however, for systems where substrate binding is tight and or
a network of hydrogen-bonding interactions exists, a complete QM/MM approach
may be more appropriate. The following Chapter “Applications of Computational
Chemistry to Selected Problems of Transition-Metal Catalysis in Biological and
Nonbiological Systems” by Hajime Hirao describes as well recent attempts to study
the structure and catalytic properties of transition metal-containing systems of
different sizes, including metalloenzymes but also metal–organic frameworks
(MOFs). Similar techniques (DFT and hybrid techniques for embedding) are used,
but examples are selected specifically and substantially broaden the spectrum of
applications, increasing the pool for critical analyses and benchmarking. The same
concerns Chapter “How Metal Coordination in the Ca-, Ce-, and Eu-Containing
Methanol Dehydrogenase Enzymes can Influence the Catalysis: A Theoretical Point
of View” written by Tiziana Marino, Mario Prejanò, and Nino Russo, where the
pool of examples is farther enriched with studies on lanthanide-containing enzymes
where relativistic effects played a significant role.
The section is finalized by Tomasz Borowski and Maciej Szaleniec in Chapter
“Challenges in Modelling Metalloenzymes” which gives a critical summary of the
entire process of constructing a reliable computational model for metalloenzymes.
This contribution, complementary to preceding chapters, nicely illustrates and
validates the key decisions and steps one has to take in such projects: validating
Preface
ix
accurate reproduction of experimental redox potentials of mono- and dinuclear
complexes, including electrocatalytically relevant systems and mixed-valence
compounds. Examples of such computational protocols that use DFT combined
with continuum solvent models, as well as a mixed, discrete-continuum approach,
are shown in this contribution. The ferrocenium/ferrocene system, widely used as
an internal standard, is discussed, followed by the presentation of intriguing
properties of mono- and bimetallic Mo/W scorpionates, in particular electrochemical communication between metal centers and a baffling dehalogenation, the
mechanism of which was elucidated only owing to the application of DFT-D3
calculations.
The end section of the book entails four chapters and discusses enzymatic and
biomimetic systems. The topic is singled out even if problems intrinsic to very large
systems incorporating transition metals are generally common; nevertheless, transition metals in bio- or bioinorganic complexes share several specific properties and
specific techniques common among them but distinctive from inorganic transition
metal complexes. This part opens with Chapter “The Quest for Accurate
Theoretical Models of Metalloenzymes: An Aid to Experiment” by Matthew G.
Quesne and Sam P. de Visser. The chapter reviews two key computational
approaches to metalloenzymes, namely quantum mechanics/molecular mechanics
(QM/MM) on complete enzyme structures and QM cluster models on active site
structures only. The former take the structure of the full enzyme with a solvent layer
into consideration, whereas the latter only include key features of the first and
second coordination sphere. The examples are discussed where the QM cluster
approach worked well; however, for systems where substrate binding is tight and or
a network of hydrogen-bonding interactions exists, a complete QM/MM approach
may be more appropriate. The following Chapter “Applications of Computational
Chemistry to Selected Problems of Transition-Metal Catalysis in Biological and
Nonbiological Systems” by Hajime Hirao describes as well recent attempts to study
the structure and catalytic properties of transition metal-containing systems of
different sizes, including metalloenzymes but also metal–organic frameworks
(MOFs). Similar techniques (DFT and hybrid techniques for embedding) are used,
but examples are selected specifically and substantially broaden the spectrum of
applications, increasing the pool for critical analyses and benchmarking. The same
concerns Chapter “How Metal Coordination in the Ca-, Ce-, and Eu-Containing
Methanol Dehydrogenase Enzymes can Influence the Catalysis: A Theoretical Point
of View” written by Tiziana Marino, Mario Prejanò, and Nino Russo, where the
pool of examples is farther enriched with studies on lanthanide-containing enzymes
where relativistic effects played a significant role.
The section is finalized by Tomasz Borowski and Maciej Szaleniec in Chapter
“Challenges in Modelling Metalloenzymes” which gives a critical summary of the
entire process of constructing a reliable computational model for metalloenzymes.
This contribution, complementary to preceding chapters, nicely illustrates and
validates the key decisions and steps one has to take in such projects: validating
Preface
ix