Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration

Upgrading of the general AMBER force field 2 for fluorinated alcohol biosolvents: A validation for water solutions and melittin solvation

The standard GAFF2 force field parameterization has been refined for the fluorinated alcohols 2,2,2-trifluoroethanol (TFE), 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), and 1,1,1,3,3,3-hexafluoropropan-2-one (HFA), which are commonly used to study proteins and peptides in biomimetic media. The structural and dynamic properties of both proteins and peptides are significantly influenced by the biomimetic environment created by the presence of these cosolvents in aqueous solutions. Quantum mechanical calculations on stable conformers were used to parameterize the atomic charges. Different systems, such as pure liquids, aqueous solutions, and systems formed by melittin protein and cosolvent/water solutions, have been used to validate the new models. The calculated macroscopic and structural properties are in agreement with experimental findings, supporting the validity of the newly proposed models.

On hidden anisotropy of formally charged fragments

The proper and precise reproduction of the molecular electrostatic potential (MEP) is crucial to describe correctly electrostatic interactions in molecular modeling. Most of the classical molecular mechanics force fields for biomolecules and drug-like molecules use the atom-centered point charges to describe MEP. However, it has been systematically pointed out in literature that such an approximation is not always enough, and some groups, like amino group or heavy halogens, require the use of anisotropic model for better description of their MEP. At the same time, the formally charged groups have not been as extensively and systematically studied as their neutral counterparts. In this report, we demonstrate that the anisotropic models for formally charged groups do bring improvements in the reference MEP reproduction, that are comparable in magnitude to those for neutral groups.

Partial charges for molecular-mechanical models of heterocyclic compounds: pyridine nitrogen

This paper deals with the effect of introducing an additional interaction site onto molecular-mechanical models of nitrogen-containing heterocyclic compounds. The introduction of only one additional site next to nitrogen atoms is shown to result in significant improvement of the quality of the models along with negligible slowdown of calculation speed. Concretely, it was proposed to introduce the site inside the aromatic ring at a distance of 0.4 Å from the nitrogen atom center. All the parametrization can be completely automated. The proposed force field allows predicting heats of evaporation of liquids of the compound under investigation with an accuracy of 1 kcal/mol.

Charge Anisotropy of Nitrogen: Where Chemical Intuition Fails

For more than half a century computer simulations were developed and employed to study ensemble properties of a wide variety of atomic and molecular systems with tremendous success. Nowadays, a selection of force-fields is available that describe the interactions in such systems. A key feature of force-fields is an adequate description of the electrostatic potential (ESP). Several force-fields model the ESP via point charges positioned at the atom centers. A major shortcoming of this approach, its inability to model anisotropies in the ESP, can be mitigated using additional charge sites. It has been shown that nitrogen is the most problematic element abundant in many polymers as well as large molecules of biological origin. To tackle this issue, small organic molecules containing a single nitrogen atom were studied. In performing rigorous scans of the surroundings of these nitrogen atoms, positions where a single extra charge can enhance the ESP description the most were identified. Significant improvements are found for ammonia, amines, and amides. Interestingly, the optimal location for the extra charge does not correlate with the chemically intuitive position of the nitrogen lone pair. In fact, the placement of an extra charge in the lone-pair location does not lead to significant improvements in most cases.

Hydrophilic and hydrophobic interactions in concentrated aqueous imidazole solutions: a neutron diffraction and total X-ray scattering study

A study of 5 M aqueous imidazole solutions combining neutron and X-ray diffraction with EPSR simulations shows dominance of hydrogen-bonding between imidazole and water and negligible hydrogen-bonding between imidazole molecules.

Synthesis of imidazo[1,2-c]thiazoles through Pd-catalyzed bicyclization of tert-butyl isonitrile with thioamides

Building new biological molecules is challenging. Herein, imidazo[1,2-c]thiazoles were synthesized as a new class of heterobicyclic analogs through Pd-catalyzed cascade bicyclization from isonitriles with thioamides. The bicyclic scaffolds were constructed by inserting three molecules of isonitrile into two molecules of thioamide and then cyclizing them in a one-pot procedure. In vitro antitumor studies of these new compounds were conducted by using the MTT assay, and compound 3c showed excellent inhibitory effects against HepG2 at 7.06 ± 0.68 μM.