Search results for "molecular dynamic"
showing 10 items of 1090 documents
Testing mode-coupling theory for a supercooled binary Lennard-Jones mixture
1995
Abstract We have performed a molecular dynamics computer simulation study to investigate the dynamical behavior of a supercooled simple liquid for comparison with the predictions of mode-coupling theory (MCT). By scaling the intermediate scattering function by the α-relaxation time r we find that the correlators fall onto a master curve extending over several decades in time. Thus we find that the time temperature superposition principle holds. In the late β-relaxation regime this master curve can be fitted very well by a master curve predicted by the idealized version MCT. However, there is no evidence for the presence of the critical decay predicted by the theory for the early part of the…
A new force field including charge directionality for TMAO in aqueous solution
2016
We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (OTMAO) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around OTMAO to mimic the OTMAO lone pairs and we migrate the negative charge on the OTMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the…
Molecular dynamics and metadynamics simulations of electrosprayed water nanodroplets including sodium bis(2-ethylhexyl)sulfosuccinate micelles.
2017
The behavior of aqueous solutions of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) under conditions of electrospray ionization (ESI) has been investigated by molecular dynamics (MD) and well-tempered metadynamics (WTM) simulations at 300 K and 400 K. We have examined water droplets with initial fixed numbers of water molecules (1000) and AOT− anions (100), and with sodium cations in the range of 70–130. At 300 K, all charged droplets show the water evaporation rate increasing with the absolute value of the initial droplet charge state (Z), accompanied by ejection of an increasing number of solvated sodium ions or by expulsion of AOT− anions depending on the sign of Z and by fragmentation i…
A quantum mechanics-molecular mechanics study of dissociative electron transfer : The methylchloride radical anion in aqueous solution
2002
The dissociative electron transfer reaction CH3Cl+e−→CH3•+Cl− in aqueous solution is studied by using a QM/MM method. In this work the quantum subsystem (a methylchloride molecule plus an electron) is described using density functional theory while the solvent (300 water molecules) is described using the TIP3P classical potential. By means of molecular dynamics simulations and the thermodynamic integration technique we obtained the potential of mean force (PMF) for the carbon–chlorine bond dissociation of the neutral and radical anion species. Combining these two free energy curves we found a quadratic dependence of the activation free energy on the reaction free energy in agreement with Ma…
Internal Structure and Dynamics of the Decamer D(ATGCAGTCAG) 2 In Li + -H 2 O Solution: A molecular Dynamics Simulation Study
2003
Molecular dynamics simulation of the decamer d(ATGCAGTCAG) 2 in aqueous solution, electroneutralized by Li + ions has been carried out. Emphasis is on the verification of the equilibrium conditions and the related structural and dynamical properties. Applicability of the kinetic part of Boltzmann's H function as a measure of thermodynamic equilibrium is tested. Overall structural stability has been confirmed by different RMSDs. Conformational and helicoidal parameters have been analyzed statistically and dynamically. Dynamical analysis reveals the existence of dynamical sub-states, which typically appear as abrupt changes from a mean level to another in the value of parameter. In statistica…
The Silica-Water Interface: How the Silanols Determine the Surface Acidity and Modulate the Water Properties.
2015
Silica is the most abundant metal oxide and the main component of the Earth's crust. Its behavior in contact with water plays a critical role in a variety of geochemical and environmental processes. Despite its key role, the details of the aqueous silica interface at the microscopic molecular level are still elusive. Here we provide such a detailed understanding of the molecular behavior of the silica-water interface, using density functional theory based molecular dynamics (DFTMD) simulations, where a consistent treatment of the electronic structure of solvent and surface is provided. We have calculated the acidity of the silanol groups at the interface directly from the DFTMD simulations,…
Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution
2015
Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (O(TMAO)) atom, due to the O-D···O(TMAO) hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···O(TMAO) hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientatio…
Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations.
2019
Using atomistic molecular dynamics simulations, we study the temperature dependence of the mechanical unfolding of a model supramolecular complex, a dimer of interlocked calixarene capsules. This system shows reversible transitions between two conformations that are stabilized by different networks of hydrogen bonds. We study the forced dissociation and formation of these networks as a function of temperature and find a strong impact of the nonequilibrium conditions imposed by pulling the system mechanically. The kinetics of the transition between the two conformations is ideally suited to investigate the range of validity of the stochastic models employed in the analysis of force dependent…
Acid–Base Properties and Surface Charge Distribution of the Water-Soluble Au102(pMBA)44 Nanocluster
2016
The pKa of the p-mercaptobenzoic acid (pMBA) ligands in the Au102(pMBA)44 nanocluster was measured by using acid–base and IR titration. The observed macroscopic pKa = 6.18 ± 0.05 is significantly more basic than that of free pMBA (pKa = 4.16), and the protonation behavior is anticooperative according to the Hill coefficient n = 0.64 ± 0.04. The cluster is truly water-soluble when more than 22 and insoluble when fewer than 7 ligands are in the deprotonated state. In order to obtain more insight into the anticooperative character, the cluster was modeled at pH ∼6.2 using constant pH molecular dynamics simulations. The pKa values of the individual pMBAs are in the range of 5.18–7.58, depending…
X-Ray crystallographic and computational study on uranyl-salophen complexes bearing nitro groups.
2017
In the solid state, salophen–UO2 complexes bearing one, two, or three NO2 groups lack the pronounced ligand curvature that represents a structural hallmark for this class of compounds. A detailed structural study based on single-crystal X-ray crystallography and computational methods, comprising molecular dynamics, gas-phase Hartree Fock, and DFT calculations, was carried out to investigate the coordination properties of the uranyl cation.