Search results for "computational studies"

Communication: anion-specific response of mesoscopic organization in ionic liquids upon pressurization

2018

One of the outstanding features of ionic liquids is their inherently hierarchical structural organization at mesoscopic spatial scales. Recently experimental and computational studies showed the fading of this feature when pressurising. Here we use simulations to show that this effect is not general: appropriate anion choice leads to an obstinate resistance against pressurization. Published by AIP Publishing.

The Catalytic Mechanism of Carboxylesterases: A Computational Study

2014

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 xenobiotics and endobiotics. They can also perform transesterification, a reaction important, for instance, in cholesterol homeostasis. The catalytic mechanisms with three different substrates (ester, thioester, and amide) have been established at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory. It was found that the reactions proceed through a mechanism involving four steps instead of two as is generally proposed: (i) nucleophilic attack of serine to the substrate, forming the first tetrahedral intermediate, (ii) formation of the ac…

A computational study to explore the molecular mechanisms behind the antiproliferative activity of Nortopsentin derivatives

2018

Synthesis, chemical characterization, computational studies and biological activity of organotin(IV) compounds interacting with enzymes involoved in …

2015

Our studies deal with the synthesis, the chemical characterization of organotin(IV) complexes of molecules, as caffeic acid, interacting with enzymes involved in epigenetic regulation.

New Bioprecursor Prodrugs of Sulfadiazine: Synthesis, X-ray Structure and Hirshfeld Analysis

2022

Sulphonamide motif is found extensively in numerous chemotherapeutic drug candidates, it acts by stopping the production of folate inside the bacterial cell. Current research has established the synthesis and characterization of new bioprecursor prodrugs of sulfadiazine. The first prodrug, 3, was synthesized via the coupling of diazonium salt of sulfadiazine with ethyl acetoacetate in AcONa at 0 °C. The second prodrug, sulfadiazine-pyrazole, 5, was furnished via cyclocondensation of the hydrazono derivative, 3, and 2-pyridyl hydrazine, 4. The generated data from the X-ray analysis is interpreted and refined to obtain the crystal structure of the target compound, 5. Density functional th…

An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge

2018

Molecular dynamics (MD) has become increasingly popular due to the development of hardware and software solutions and the improvement in algorithms, which allowed researchers to scale up calculations in order to speed them up. MD simulations are usually used to address protein folding issues or protein-ligand complex stability through energy profile analysis over time. In recent years, the development of new tools able to deeply explore a potential energy surface (PES) has allowed researchers to focus on the dynamic nature of the binding recognition process and binding-induced protein conformational changes. Moreover, modern approaches have been demonstrated to be effective and reliable in …

Role of Weak Hydrogen Bonds and Halogen Bonds in 5-Halo-1,3-dimethyluracils and Their Cocrystals—A Combined Experimental and Computational Study

2016

Seven single crystals containing either N,N-dimethyluracil (DMHU) or one of its 5-halogenated derivatives (DMXU; X = F, Cl, Br, I) were prepared using N,N-dimethylformamide as the crystallization solvent. Single crystal X-ray diffraction and quantum chemical calculations carried out at the spin component scaled local MP2 level of theory were then used to study the intramolecular halogen and nonconventional hydrogen bonds present in the structures. The results were compared to and contrasted with the previously reported data for uracil and its halogenated derivatives. In particular, the intermolecular interactions in DMIU were compared to the halogen and hydrogen bonds in 5-iodouracil that, …