[HTML][HTML] The ONIOM method and its applications

LW Chung, WMC Sameera, R Ramozzi… - Chemical …, 2015 - ACS Publications
The fields of theoretical and computational chemistry have come a long way since their
inception in the mid-20th century. Fifty years ago, only rudimentary approximations for very …

Computational enzymatic catalysis

MJ Ramos, PA Fernandes - Accounts of chemical research, 2008 - ACS Publications
Computational methodologies are playing increasingly important roles in elucidating and
presenting the complete and detailed mechanisms of enzymatic reactions because of their …

Understanding ribonucleotide reductase inactivation by gemcitabine

NM Cerqueira, PA Fernandes… - Chemistry–A European …, 2007 - Wiley Online Library
This paper focuses on the inhibition of ribonucleotide reductase (RNR) by gemcitabine, 2′,
2′‐difluoro‐2′‐deoxycytidine (dFdC), a deoxycytidine analogue that is a very active drug …

Gemcitabine: a critical nucleoside for cancer therapy

D S. Gesto, N MFSA Cerqueira… - Current medicinal …, 2012 - benthamdirect.com
Gemcitabine (dFdC, 2', 2'-difluorodeoxycytidine) is a deoxycytidine nucleoside analogue of
deoxycytidine in which two fluorine atoms have been inserted into the deoxyribose ring. Like …

The carboxylate shift in zinc enzymes: A computational study

SF Sousa, PA Fernandes… - Journal of the American …, 2007 - ACS Publications
Zinc is the second most abundant transition element in biology and the only metal known to
be represented in enzymes from each one of the six classes established by the International …

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

CS Mota, MG Rivas, CD Brondino, I Moura… - JBIC Journal of …, 2011 - Springer
Metal-dependent formate dehydrogenases (Fdh) from prokaryotic organisms are members
of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and …

Selective transformations of carbohydrates inspired by radical-based enzymatic mechanisms

CE Suh, HM Carder, AE Wendlandt - ACS Chemical Biology, 2021 - ACS Publications
Enzymes are a longstanding source of inspiration for synthetic reaction development.
However, enzymatic reactivity and selectivity are frequently untenable in a synthetic context …

The catalytic mechanism of carboxylesterases: a computational study

J Aranda, N Cerqueira, PA Fernandes, M Roca… - Biochemistry, 2014 - ACS Publications
The catalytic mechanism of carboxylesterases (CEs, EC 3.1. 1.1) is explored by
computational means. CEs hydrolyze ester, amide, and carbamate bonds found in …

Ribonucleotide reductase: a critical enzyme for cancer chemotherapy and antiviral agents

NM Cerqueira, PA Fernandes… - Recent patents on anti …, 2007 - ingentaconnect.com
Ribonucleotide Reductase (RNR) plays a critical role in DNA synthesis, and is a well-
recognized target for cancer chemotherapeutic and antiviral agents. RNR inhibition …

Unraveling the Enigmatic Mechanism of l-Asparaginase II with QM/QM Calculations

DS Gesto, NM Cerqueira, PA Fernandes… - Journal of the …, 2013 - ACS Publications
In this paper, we have studied the catalytic mechanism of l-asparaginase II computationally.
The reaction mechanism was investigated using the ONIOM methodology. For the geometry …