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1.
J Chem Theory Comput ; 19(21): 7685-7694, 2023 Nov 14.
Article in English | MEDLINE | ID: mdl-37862602

ABSTRACT

In this study, the use of self-consistent field quasi-diabats is investigated for calculation of triplet energy transfer diabatic coupling elements. It is proposed that self-consistent field quasi-diabats are particularly useful for studying energy transfer (EnT) processes because orbital relaxation in response to changes in electron configuration is implicitly built into the model. The conceptual model that is developed allows for the simultaneous evaluation of direct and charge-transfer mechanisms to establish the importance of the different possible EnT mechanisms. The method's performance is evaluated using two model systems: the ethylene dimer and ethylene with the methaniminium cation. While states that mediate the charge-transfer mechanism were found to be higher in energy than the states involved in the direct mechanism, the coupling elements that control the kinetics were found to be significantly larger in the charge-transfer mechanism. Subsequently, we discuss the advantage of the approach in the context of practical difficulties with the use of established approaches.

2.
Methods Enzymol ; 669: 119-150, 2022.
Article in English | MEDLINE | ID: mdl-35644169

ABSTRACT

Nature employs two biologically active forms of vitamin B12, adenosylcobalamin (or coenzyme B12) and methylcobalamin, as cofactors in molecular transformations both in bacteria and mammals. Computational chemistry, guided by experimental data, has been used to explore fundamental characteristics of these enzymatic reactions. In particular, the quantum mechanics/molecular mechanics (QM/MM) method has proven to be a powerful tool in elucidating important characteristics of B12-dependent enzymatic reactions. Herein, we will present a brief tutorial in conducting QM/MM calculations for B12 enzymatic reactions. We will summarize recent contributions that target the use of QM/MM calculations in both photochemical and enzymatic reactions including AdoCbl-dependent ethanolamine ammonia lyase, glutamate mutase, and photoreceptor CarH.


Subject(s)
Cobamides , Computational Biology , Animals
3.
ChemSusChem ; 14(13): 2704-2709, 2021 Jul 06.
Article in English | MEDLINE | ID: mdl-33974355

ABSTRACT

A reversible Van der Waals complex formation between the electron-deficient fluorinated aromatic ring and N,N-dimethylformamide (DMF) molecules followed by light irradiation resulted in charge transfer (CT) process. The complex was stabilized by ammonium formate and further decomposed to form the C-N bond. Control experiments revealed that the simultaneous SN Ar pathway also contributes to product formation. This methodology is mild, metal-free, and effective for the amination of a variety of substrates. The reproducibility of this methodology was also verified on gram-scale reactions. The CT states were supported by control UV/Vis spectroscopy and computational studies.

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