Conformational Solvation Studies of LIGNOLs with Molecular Dynamics and Conductor-Like Screening Model
نویسندگان
چکیده
Molecular dynamics (MD) simulations were performed on sterically hindered α-conidendrin-based chiral 1,4-diols (LIGNOLs) from the naturally occurring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behaviour of the LIGNOLs in aqueous solution adopting the TIP4P model. The topologies of the LIGNOLs were constructed manually and they were modeled with the OPLS-AA force field implemented in GROMACS. The four most relevant torsional angles in the LIGNOLs were properly analyzed during the simulations. The determining property for the conformation preferred in aqueous solution was found to be the lowest energy in gas phase. The solvation effects on the LIGNOLs were also studied by quantum chemical calculations applying the COnductor-like Screening MOdel (COSMO). The hydration studies of the MD simulations showed that several of these LIGNOLs, produced from a renewable source, have a great potential of acting as chiral catalysts.
منابع مشابه
Molecular Docking Based on Virtual Screening, Molecular Dynamics and Atoms in Molecules Studies to Identify the Potential Human Epidermal Receptor 2 Intracellular Domain Inhibitors
Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family having tyrosine kinase activity. Overexpression of HER2 usually causes malignant transformation of cells and is responsible for the breast cancer. In this work, the virtual screening, molecular docking, quantum mechanics and molecular dynamics methods were employed to study protein–ligand ...
متن کاملStudies of Interaction between Propranolol and Human Serum Albumin in the Presence of DMMP by Molecular Spectroscopy and Molecular Dynamics Simulation
The interaction between propranolol (PROP) and human serum albumin (HSA) was studied in the presence of dimethyl methylphosphonate (DMMP). DMMP is usually considered as a simulant for chemical warfare agents (CWAs). For this purpose fluorescence quenching, resonance light scattering (RLS), synchronous, three-dimensional fluorescence spectroscopy and molecular dynamics (MD) simulation were emplo...
متن کاملSpectroscopic, Docking and Molecular Dynamics Simulation Studies on the Interaction of Etofylline and Human Serum Albumin
The purpose of this study is to investigate the interaction of Etofylline as an established drug for asthma remedy, with the major transport protein in human blood circulation, the human serum albumin (HSA). In this respect, the fluorescence and circular dichroism (CD) spectroscopy techniques, along with the molecular docking and molecular dynamics simulation methods were employed. Analysis of ...
متن کاملPrediction of accurate pKa values of some α-substituted carboxylic acids with low cost of computational methods
The acidity constants (pKa) of thirty four (34) ;-substituted carboxylic acids in aqueous solution havebeen calculated using conductor-like polarizable continuum (C-PCM) solvation model. The gasphaseenergies at the Density Functional Theory (DFT-MPW1PW91) and solvation energies atHartree Fock (HF) are combined to estimate the pKa values which are very close to the experimentalvalues where, and ...
متن کاملUniversal solvation model based on conductor-like screening model
Atomic surface tensions are parameterized for use with solvation models in which the electrostatic part of the calculation is based on the conductor-like screening model (COSMO) and the semiempirical molecular orbital methods AM1, PM3, and MNDO/d. The convergence of the calculated polarization free energies with respect to the numerical parameters of the electrostatic calculations is first exam...
متن کامل