Atomistic approaches in modern biology: from quantum by Luca Bertini, Maurizio Bruschi, Luca de Gioia (auth.),

By Luca Bertini, Maurizio Bruschi, Luca de Gioia (auth.), Markus Reiher (eds.)

"From the reviews:"

This booklet is concentrated on computational molecular modeling and its functions in biology and is very priceless in respects. First, the reader will take pleasure in vast but specific assurance of contemporary theoretical methods to the buildings, digital houses, and dynamical behaviour of peptides, metalloenzymes, bioinorganic structures, proteins, and nucleic acids. additionally incorporated are very good methods-oriented chapters considering Qm/MM tools, Car-Parinello molecular dynamics, and classical dynamics of biomolecules close to transition states. moment, the writing and modifying are of uniformly top of the range. each one bankruptcy is a worthwhile and well timed element of access to the literature of the subfield of computational chemistry that's being lined. a few chapters specialise in the authors’ personal contributions, while others are broader and extra inclusive in scope, yet all are tremendous well-written and the authors do an exceptional activity of putting their very own paintings in a bigger context – anything usually now not accomplished in assessment sequence. … total, this quantity constitutes a superb contribution to the themes in present Chemistry sequence.

(Robert Q. Topper, Monmouth college, JA076953F, 10.1021/ja076953f)

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88 ture characterized by a µ-CO group. The gas-phase geometry optimization of the [(CH3 S)4 (Fe4 S4 )(PDT)(Fe2 )(µ-CO)(CO)2 (CN)2 ]–5 isomer 5a1 , reveals that this species is unstable. However, the same complex is stable when the optimization is carried out in presence of a polarizable continuum medium 5a4 and 5a40 . In this case the electronic structure of the [Fe4 S4 ] cluster is very similar to that calculated for 5b4 , being still compatible with a formal Fe(III)Fe(II)Fe(II)Fe(II) redox state and with the Fe(I)Fe(I) redox state of the [2Fe]H cluster.

6 Conclusions and Perspectives The application of quantum chemical methods to the investigation of hydrogenases and related biomimetic models has nicely complemented experimental studies, allowing us to disclose key factors related to the catalytic properties of the enzymes. In particular, the possibility to use theoretical methods to study intermediate and transition state structures, reaction energies and activation barriers, as well as spectroscopic properties, has allowed us to dissect the molecular mechanism of several reaction paths relevant to hydrogenase chemistry.

Among GGA functionals, the Becke–Perdew (BP86) exchange-correlation functional is one of the most used. This functional is composed by the Becke88 exchange [23] and the Perdew GGA correlation [24] terms. Another important approach to built DFT functionals is the so-called hybrid method based on the adiabatic connection formula [186]. According to the latter, the exact Exc functional is given by the following integral: 1 ψλ |vxc (λ)|ψλ dλ , Exc = (35) 0 where λ is the parameter defined in the Hamiltonian operator in Eq.

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