All-atom molecular dynamics simulations for benzene-water mixtures are performed, aiming to explore the relationship between the microscopic structures and the thermodynamic properties, in particular, the transformation dynamics from the mutually soluble state to the phase-separated state. We find that the molecular aggregation of benzene in the water-rich mixture is distinctly different from that of water in the benzene-rich mixture. This aggregation difference is attributed to the different intermolecular interactions: the clustering of benzene molecules in the water-rich mixture is primarily driven by weak short-distance π-π interactions; while the formation of water clusters in the benzene-rich solution is triggered by long-range dipole-dipole electrostatic interactions. Moreover, the molecular aggregations show double-scaled features: firstly assembling in a quasi-plane at a low concentration, then bulking in three dimensions with an increase in concentration.
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http://dx.doi.org/10.1039/c4cp01537a | DOI Listing |
J Chem Inf Model
November 2021
Department of Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049 Madrid, Spain.
The lack of conformational sampling in virtual screening projects can lead to inefficient results because many of the potential drugs may not be able to bind to the target protein during the static docking simulations. Here, we performed ensemble docking for around 2000 United States Food and Drug Administration (FDA)-approved drugs with the RNA-dependent RNA polymerase (RdRp) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a target. The representative protein structures were generated by clustering classical molecular dynamics trajectories, which were evolved using three solvent scenarios, namely, pure water, benzene/water and phenol/water mixtures.
View Article and Find Full Text PDFPhys Chem Chem Phys
June 2018
School of Physical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK.
We present results of a combined vacuum ultraviolet (VUV) and infrared (IR) photoabsorption study of amorphous benzene : water mixtures and layers to investigate the benzene-water interaction in the solid phase. VUV spectra of 1 : 1, 1 : 10 and 1 : 100 benzene : water mixtures at 24 K reveal a concentration dependent shift in the energies of the 1B2u, 1B1u and 1E1u electronic states of benzene. All the electronic bands blueshift from pure amorphous benzene towards gas phase energies with increasing water concentration.
View Article and Find Full Text PDFJ Phys Chem B
May 2018
Department of Chemical Engineering , University of California, Santa Barbara , Santa Barbara , California , United States.
Bottom-up coarse-grained (CG) models are now regularly pursued to enable large length and time scale molecular simulations of complex, often macromolecular systems. However, predicting fluid phase equilibria using such models remains fundamentally challenging. A major problem stems from the typically low transferability of CG models beyond the densities and/or compositions at which they are parametrized, which is necessary if they are to describe distinct structural and thermodynamic properties unique to each phase.
View Article and Find Full Text PDFPhys Chem Chem Phys
October 2014
Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
All-atom molecular dynamics simulations for benzene-water mixtures are performed, aiming to explore the relationship between the microscopic structures and the thermodynamic properties, in particular, the transformation dynamics from the mutually soluble state to the phase-separated state. We find that the molecular aggregation of benzene in the water-rich mixture is distinctly different from that of water in the benzene-rich mixture. This aggregation difference is attributed to the different intermolecular interactions: the clustering of benzene molecules in the water-rich mixture is primarily driven by weak short-distance π-π interactions; while the formation of water clusters in the benzene-rich solution is triggered by long-range dipole-dipole electrostatic interactions.
View Article and Find Full Text PDFJ Mol Model
March 2013
KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China.
A combined and sequential use of quantum mechanical (QM) calculations and classical molecular dynamics (MD) simulations was made to investigate the σ and π types of hydrogen bond (HB) in benzene-water and pyrrole-water as clusters and as their liquid mixture, respectively. This paper aims at analyzing similarities and differences of these HBs resulted from QM and MD on an equal footing. Based on the optimized geometry at ωb97xD/aug-cc-pVTZ level of theory, the nature and property of σ and π types of HBs are unveiled by means of atoms in molecules (AIM), natural bond orbital (NBO) and energy decomposition analysis (EDA).
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