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The formation of the Hg-N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H O) ] , (2) T + [Hg(H O) (OH)] , (3) T + Hg(H O) (OH) , and (4) N3-deprotonated T + Hg(H O) (OH) . The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4-5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.
This article was published in the following journal.
Name: Journal of computational chemistry
Ultraviolet rays induce interstrand and intrastrand DNA cross-links, usually thymine-thymine cyclobutane dimer (T-T) and thymine-thymine pyrimidine-pyrimidone (6-4) photoproduct (T (6-4) T). These DNA...
Mastering artificial water oxidation is a key step on moving away from fossil fuels toward a carbon emission-free society. Unfortunately, the crucial chemical transformation of this reaction, the O-O ...
A previous study suggested that a thymine (THY) challenge dose could detect aberrant pharmacokinetics in known cases of fluoropyrimidine toxicity compared with healthy volunteers. The preliminary data...
We have developed an enhanced conformational sampling method combining replica-exchange umbrella sampling (REUS) with Gaussian accelerated molecular dynamics (GaMD). REUS enhances the sampling along p...
Nickel complexes have been widely employed as catalysts in C-C and C-heteroatom bond formation reactions. While Ni(0), Ni(i), and Ni(ii) intermediates are most relevant in these transformations, recen...
The Veterans Health Administration (VHA) has stated the need for a brief screening instrument that can assist with the triage of the enormous number of returning OEF/OIF veterans with conc...
The purpose of this study is to compare the clinical performance of three dental adhesive systems used to bond Class V cavity fillings in adult teeth.
The mechanisms underlying the formation and composition of gingival crevicular fluid (GCF) and its flow into and from periodontal pockets are not understood very well. The aim of this stud...
BACKGROUND: Pulmonary embolism (PE) is associated to high mortality rate worldwide. However, the diagnosis of PE often results inaccurate. Many cases of PE are incorrectly diagnosed or mis...
This trial is referred to as the "umbrella trial". The BATTLE program consists of this umbrella trial plus four phase II protocols into which the umbrella patients are enrolled. Patients ...
An enzyme that removes THYMINE and URACIL bases mispaired with GUANINE through hydrolysis of their N-glycosidic bond. These mispaired nucleotides generally occur through the hydrolytic DEAMINATION of 5-METHYLCYTOSINE to thymine.
A sampling methodology using small sample sizes when conducting surveys in small geographical or population-based areas or lots.
Sampling of blood levels of the adrenocorticotropic hormone (ACTH) by withdrawal of blood from the inferior petrosal sinus. The inferior petrosal sinus arises from the cavernous sinus and runs to the internal jugular vein. Sampling of blood at this level is a valuable tool in the differential diagnosis of Cushing disease, Cushing syndrome, and other adrenocortical diseases.
A class of enzymes that catalyze the formation of a bond between two substrate molecules, coupled with the hydrolysis of a pyrophosphate bond in ATP or a similar energy donor. (Dorland, 28th ed) EC 6.
A method for diagnosis of fetal diseases by sampling the cells of the placental chorionic villi for DNA analysis, presence of bacteria, concentration of metabolites, etc. The advantage over amniocentesis is that the procedure can be carried out in the first trimester.