A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach.

The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities.

New Way for Probing Bond Strength.

The covalent chemical bond is intimately linked to electron sharing between atoms. The recent independent gradient model (IGM) and its δ descriptor provide a way to quantify locally this electron density interpenetration from wavefunction calculations. Each bond has its own IGM-δ signature.

Atomic Decomposition Scheme of Noncovalent Interactions Applied to Host-Guest Assemblies.

The design of novel stimuli-responsive supramolecular systems based on host-guest chemistry implies a thorough understanding of the noncovalent interactions involved. In this regard, some computational tools enabling the extraction of the noncovalent signatures from local descriptors based on the electron density have been previously proposed. Although very useful to detect the existence of such interactions, these analyses provide only a semi-quantitative description, which represents a limitation.

The Independent Gradient Model: A New Approach for Probing Strong and Weak Interactions in Molecules from Wave Function Calculations.

Extraction of the chemical interaction signature from local descriptors based on electron density (ED) is still a fruitful field of development in chemical interpretation. In a previous work that used promolecular ED (frozen ED), the new descriptor, δg , was defined. It represents the difference between a virtual upper limit of the ED gradient (∇ρIGM , IGM=independent gradient model) that represents a noninteracting system and the true ED gradient (∇ρ ).

Development of the first model of a phosphorylated, ATP/Mg-containing B-Raf monomer by molecular dynamics simulations: a tool for structure-based design.

A model of phosphorylated and ATP-containing B-Raf protein kinase is needed as a tool for the structure-based design of new allosteric inhibitors, since no crystal structure of such a system has been resolved. Here, we present the development of such a model as well as a thorough analysis of its structural features. This model was prepared using a systematic molecular dynamics approach considering the presence or absence of both the phosphate group at the Thr599 site and the ATP molecule.

Accurately extracting the signature of intermolecular interactions present in the NCI plot of the reduced density gradient versus electron density.

An electron density (ED)-based methodology is developed for the automatic identification of intermolecular interactions using pro-molecular density. The expression of the ED gradient in terms of atomic components furnishes the basis for the Independent Gradient Model (IGM). This model leads to a density reference for non interacting atoms/fragments where the atomic densities are added whilst their interaction turns off.

GPU accelerated implementation of NCI calculations using promolecular density.

The NCI approach is a modern tool to reveal chemical noncovalent interactions. It is particularly attractive to describe ligand-protein binding. A custom implementation for NCI using promolecular density is presented.