Search results for "molecular dynamics"
showing 10 items of 1075 documents
Understanding the microscopic origin of gold nanoparticle anisotropic growth from molecular dynamics simulations.
2013
We use molecular dynamics simulations in order to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. We provide the first atomistic model of different surfaces on gold nanoparticles in a growing electrolyte solution, and we describe the interaction of the metal with the surfactants, namely, cetyltrimethylammonium bromide (CTAB) and the ions. An innovative aspect is the inclusion of the role of the surfactants, which are explicitly modeled. We find that on all the investigated surfaces, namely, (111), (110), and (100), CTAB forms a layer of distorted cylindrical micelles where channels among micelles provide direct ion access to the surface. In particular,…
Dynamic Molecular Graphs: “Hopping” Structures
2013
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscen…
Crystalline self-assembly induced by aromatic edge-to-face interactions: the crystal structure of 2,6,6,10-tetrabenzyl-2,10-diaza-6-azonia[11]paracyc…
2002
The crystal structure of 2,6,6,10-tetrabenzyl-2,10-diaza-6-azonia[11]paracyclophane bromide reveals several intermolecular aromatic edge-to-face interactions which are important in the three-dimensional growing of the crystalline structure. Molecular dynamics and semiempirical studies indicate that the conformer found in the crystal is not the most stable in solution confirming the important role that edge-to-face interactions play in the structural arrangement found in the solid state.
Negative thermal expansion of quartz glass at low temperatures: An ab initio simulation study
2017
Abstract Using a mixed classical Molecular dynamics (MD)/ab initio simulation scheme combined with a quasi-harmonic approximation, we calculate the linear thermal expansion coefficient αL(T) in vitreous silica glasses. The systems are first cooled down by classical MD simulations. Then they are structurally relaxed by ab initio DFT calculations. The vibrational properties are calculated employing the frozen phonon method, and these results are finally used to calculate the Helmholtz free energy as a function of volume. In agreement with experiments, our simulations predict that αL(T) is negative at low temperatures up to T ≈ 150 K. In this low-temperature regime, the simulation results are …
High precision numerical estimates of acoustic phonon frequencies of nonspherical nanoparticles
2006
We introduce an adapted method for calculating the acoustic vibrational frequencies of arbitrarily shaped nanoparticles to high precision. Molecular dynamics simulation results are tested against exact solutions for a free sphere, a hollow sphere and a spheroid. This permits theoretical predictions of the frequencies of peaks in low frequency Raman spectra. Our results demonstrate that vibrational frequencies can be calculated for a wide range of low frequency modes with accuracies on the order of a tenth of a percent.
Self-assembly and rheology of dipolar colloids in simple shear studied using multi-particle collision dynamics.
2017
Magnetic nanoparticles in a colloidal solution self-assemble in various aligned structures, which has a profound influence on the flow behavior. However, the precise role of the microstructure in the development of the rheological response has not been reliably quantified. We investigate the self-assembly of dipolar colloids in simple shear using hybrid molecular dynamics and multi-particle collision dynamics simulations with explicit coarse-grained hydrodynamics, conduct simulated rheometric studies and apply micromechanical models to produce master curves, showing evidence of the universality of the structural behavior governed by the competition between the bonding (dipolar) and erosive …
Direct Evidence of the Amino Acid Side Chain and Backbone Contributions to Protein Anharmonicity
2010
Elastic incoherent neutron scattering has been used to study the temperature dependence of the mean-square displacements of nonexchangeable hydrogen atoms in powders of a series of homomeric polypeptides (polyglycine, polyalanine, polyphenylalanine and polyisoleucine) in comparison with myoglobin at the same hydration level (h = 0.2). The aim of the work was to measure the dynamic behavior of different amino acid residues separately and assess the contribution of each type of side chain to the anharmonic dynamics of proteins. The results provide direct experimental evidence that the first anharmonic activation, at approximately 150 K, is largely due to methyl group rotations entering the ti…
1H,13C and17O NMR study of substituted nitropyridines
1991
1H, 13C and 17O NMR spectra for 22 substituted nitropyridines were measured and their 1H NMR spectra were analysed. The most significant variations in the NMR parameters are found for isomeric hydroxy derivatives, owing to the possibility of keto–enol tautomerism. The prevalence of the keto form is observed in 2- and 4-hydroxy derivatives, while the 3-hydroxy derivative exists in its enol form. Among the three nuclei studied, 17O seems to be the best nucleus for probing the keto–enol tautomerism. No correlation is observed between the torsion angle of the nitro group and its 17O NMR chemical shift. Molecular mechanics calculations were performed to clarify the torsional energetics of the ni…
Molecular Dynamics of CH
2019
We theoretically investigate graphene layers, proposing them as membranes of subnanometer size suitable for CH4/N2 separation and gas uptake. The observed potential energy surfaces, representing the intermolecular interactions within the CH4/N2 gaseous mixtures and between these and the graphene layers, have been formulated by adopting the so-called Improved Lennard-Jones (ILJ) potential, which is far more accurate than the traditional Lennard-Jones potential. Previously derived ILJ force fields are used to perform extensive molecular dynamics simulations on graphene's ability to separate and adsorb the CH4/N2 mixture. Furthermore, the intramolecular interactions within graphene were explic…
The Structure of Cholesterol in Lipid Rafts
2014
Rafts, or functional domains, are transient nano- or mesoscopic structures in the plasma membrane and are thought to be essential for many cellular processes such as signal transduction, adhesion, trafficking and lipid/protein sorting. Observations of these membrane heterogeneities have proven challenging, as they are thought to be both small and short-lived. With a combination of coarse-grained molecular dynamics simulations and neutron diffraction using deuterium labeled cholesterol molecules we observe raft-like structures and determine the ordering of the cholesterol molecules in binary cholesterol-containing lipid membranes. From coarse-grained computer simulations, heterogenous membra…