Molecular modeling

Calculations were done by applying the B3LYP/6-31++G(d) method on the zwitterionic L-diglycine and L-dialanine to study the solvent effects on their structures and vibrational features. Three models of solvation (implicit, explicit, and explicit in implicit) were used and the subsequent resulting values compared. Even though both dipeptides surrounded by 12 water molecules seem sufficient to stabilize their zwitterionic characters, notably to avoid the proton transfer between the backbone (N t H[Formula: see text], COO (-)) groups, the hybrid model of solvation (explicit in implicit noted 12W/Continuum) appears to be in better agreement with available IR and Raman experiments than explicit and implicit models. The harmonic vibrational modes derived from geometry optimization of L-diglycine and L-dialanine in 12W/Continuum, agree with the available IR and Raman experimental values within 1 % for L-diglycine and 2 % for L-dialanine, and they appear more accurate than those found using the explicit model (12W). Graphical Abstract DFT/6-31++G∗ Optimized structures of L-diglycine (top) and L-dialanine (bottom) surrounded by 12 water molecules all embedded in a continuum.

In this work, we simulated modified organoclay exfoliation and intercalation at an atomistic level, thus providing information about the rational choice of compatibilizers and polymer insertions behavior. Phase morphology and segregation domains have then been obtained ...

The medium and far IR spectra of the title compounds are discussed and related to the molecular structure. The spectral analysis is supported by a normal coordinate treatment based on a simplified molecular model. Bands near 375 and 290 cm−1 are assigned to the Co-O and Co-N stretching vibrations, respectively; the corresponding force constants are estimated to be 1.11 and

Mixed lineage leukemia (MLL) is an aggressive form of leukemia that affects both infants and adults and typically carries a poor prognosis. The underlying genetic defect is a chromosomal translocation that fuses the MLL gene to a variety of partners, and the resulting oncogenic fusion proteins gain the ability to interact with at least 3 known protein complexes, one of which contains DOT1L, a histone methyltransferase that catalyzes the methylation of histone H3 (H3K79). As DOT1L is essential for leukemic transformation, small-molecule inhibitors of DOT1L function are an attractive therapeutic target for this type of leukemia.
As per the previous researches show anti-cancer activity of Pyrazolone we have presumed that derivates of this moeity can be good inhibitor for DOT1L. With the help of virtual screening and molecular docking approach using Lamarckian Genetic Algorithm we have performed the binding mode of derivates of Pyrazolone with DOT1L.

The study involved virtual screening of 6000 molecules on the basis of structure similarity of Pyrazolone from different chemical databases. Molecular docking using Lamarckian Genetic Algorithm was carried out for these ligands and the result gave binding energies which were in the range of -11.18 kcal/mol to -1.25 kcal/mol. The top molecules were selected on the basis of minimum binding energy and protein-ligand complex was created. They were then visualized using UCSF chimera for H-bond interaction between ligand and active site residues of DOT1L which resulted in finding intricate atomic scale properties between ligand and residues PHE 223, ASP 161 and GLU 186. The top molecules then were run for in-silico ADMET and druglikeness properties in which we got promising results.  Further in-vitro and in-vivo study is required on these molecules to test the inhibition of DOT1L.

The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler’s cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models’ materiality contributing to the solving of the molecule’s structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations.

Photochromic compounds exhibit reversible transition between closed and open isomeric forms upon irradiation accompanied by change in their color. The two isomeric forms differ not only in absorption spectra, but also in various physical and chemical properties and find applications as optical switching and data storage materials. In this contribution we apply Density Functional Theory (DFT) and Time-Dependent DFT (TD-DFT) to predict the equilibrium geometry and absorption spectra of a benchmark set of diarylethene based photochromic compounds in open and closed forms (before and after photocyclization). Comparison of the calculated Bond Length Alternation parameters with those available from the X-ray data indicates M05-2x functional to be the best method for geometry optimization when basis set includes polarization functions. We found M05 functional accurately predicts the maximum absorption wavelength when solvent is taken into account. We recommend combined theory level TD-M05/...

Quaternions are an important tool to describe the orientation of a molecule. This paper considers the use of quaternions in matching two conformations of a molecule, in interpolating rotations, in performing statistics on orientational data, in the random sampling of rotations, and in establishing grids in orientation space. These examples show that many of the rotational problems that arise in molecular modeling may be handled simply and efficiently using quaternions.