the conformational analysis of the organic compounds specially the biologically active natural products has attracted the consideration of different research groups. therefore, in the present study the mp2/6-311+g(d,p)//b3lyp/6-311+g(d,p) level of theory was used to study the conformations of dapdiamide d. the identity of interactions in selected conformers was studied using atom in molecule ap...

The conformational analysis of the organic compounds specially the biologically active natural products has attracted the consideration of different research groups. Therefore, in the present study the MP2/6-311+g(d,p)//B3LYP/6-311+g(d,p) level of theory was used to study the conformations of dapdiamide D. The identity of interactions in selected conformers was studied using atom in molecule ap...

more recently medical chemistry research has been focused on proteins that drive and controlcell cycle progression. among them, the cyclin dependent kinases (cdk’s) are a group ofserine/threonine kinases, which rule the transition between successive stages of the cell cycle. theactivity of cdk’s is regulated by multiple mechanisms, including binding to cyclins, which is a broadclass of positive...

Ab initio calculations at HF/6-31G* level of theory for geometry optimization and MP2/6-31G*//HF/6-31G* for a single point total energy calculation are reported for the importantenergy-minimum conformations and transition-state geometries of 1, 3-diazacyclohepta-1, 2-diene (2) and 1, 3-diazacycloocta-1, 2-diene (3). The C2 symmetric twist-chair (2-TC)conformation of 2 is calculated to be 7.4 kJ...

nbo analysis and density functional theory (dft: b3lyp/6-311+g**) based method were used to study the impacts of the anomeric effects (ae) on the conformational properties of 2-methoxy-1,2,4,5-tetrahydro-benzo[d]oxepine (1), -thiepine (2) and -selenepine (3). the gibbs free energy difference (geq–gax) values (i.e. δgeq-ax) at 298.15 k and 1 atm between the axial and equatorial conformations inc...

NBO analysis and density functional theory (DFT: B3LYP/6-311+G**) based method were used to study the impacts of the anomeric effects (AE) on the conformational properties of 2-methoxy-1,2,4,5-tetrahydro-benzo[d]oxepine (1), -thiepine (2) and -selenepine (3). The Gibbs free energy difference (Geq–Gax) values (i.e. ΔGeq-ax) at 298.15 K and 1 atm between the axial and equatorial conformations inc...

RNA structure heterogeneity is a major challenge when querying structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting conformations from mutational profiling experiments. Analysis SARS-CoV-2 genome using dimethyl sulfate sequencing (DMS-MaPseq) and identifies multiple regions that fold into two mutually exclusive conformations, including conserved...

The energy minimization of a small molecule alone does not automatically stop at a local minimum of the potential energy surface of the molecule if the minimum is shallow, thus leading to folding of the molecule and consequently hampering the generation of the bound conformation of a guest in the absence of its host. This questions the practicality of virtual screening methods that use conforma...