Effect of double bonds on the dynamics of hydrocarbon chains

©1992 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/97/1240/1DOI:10.1063/1.463250Brownian dynamics simulations of isolated 18-carbon chains have been performed, both for saturated and unsaturated hydrocarbons. The effect of one or several (nonconjugated) double bonds on the properties of the chains is discussed in terms of both equilibrium and dynamic properties. The introduction of a cis double bond increases the relaxation rates of the unsaturated chain with respect to the saturated alkane. On the other hand, coupling effects in the torsional transitions around a trans double bond make the dynamics of this unsaturated chain very similar to the saturated one. Based on these results, the parameters and moves of a dynamic Monte Carlo algorithm are tuned to reproduce the observed behavior, providing an efficient method for the study of more complicated systems

Chlorine Adsorption on Graphene: Chlorographene

We perform first-principles structure optimization, phonon frequency and finite temperature molecular dynamics calculations based on density functional theory to study the interaction of chlorine atoms with graphene predicting the existence of possible chlorinated graphene derivatives. The bonding of a single chlorine atom is ionic through the transfer of charge from graphene to chlorine adatom and induces negligible local distortion in the underlying planar graphene. Different from hydrogen and fluorine adatoms, the migration of a single chlorine adatom on the surface of perfect graphene takes place almost without barrier. However, the decoration of one surface of graphene with Cl adatoms leading to various conformations cannot sustain due to strong Cl-Cl interaction resulting in the desorption through the formation of Cl$_2$ molecules. On the contrary, the fully chlorinated graphene, chlorographene CCl, where single chlorine atoms are bonded alternatingly to each carbon atom from different sides of graphene with $sp^3$-type covalent bonds, is buckled. We found that this structure is stable and is a direct band gap semiconductor, whose band gap can be tuned by applied uniform strain. Calculated phonon dispersion relation and four Raman-active modes of chlorographene are discussed.Comment: http://pubs.acs.org/doi/abs/10.1021/jp307006

Zipping and unzipping of nanoscale carbon structures

We demonstrate theoretically that hydrogenation and annealing applied to nanoscale carbon structures play a crucial role in determining the final shape of the system. In particular, graphene flakes characterized by the linear and non-hydrogenated zigzag or armchair edges have high propensity to merge into a bigger flake or a nanotube (the formation of a single carbon-carbon bond lowers the total energy of the system by up to 6.22 eV). Conversely, the line of the $sp^2$ carbon bonds (common for pure carbon structures such as graphene or a carbon nanotube) converted into the $sp^3$ type by hydrogenation shows an ability to disassemble the original structure by cutting it along the line of the modified bonds. These structural transformations provide us with an understanding of the behavior of mobile carbon structures in solution and a distinct scenario of how to preserve the original structure which would be a crucial issue for their application in carbon-based electronics.Comment: 7 pages, 6 figure

Characteristic of silicon doped diamond like carbon thin films on surface properties and human serum albumin adsorption

Diamond-like carbon (DLC) coatings are useful for creating biocompatible surfaces for medical implants. DLC and silicon doped DLC have been synthesised using plasma enhanced chemical vapour deposition (PECVD). The effects of surface morphology on the interaction of human serum albumin (HSA) with doped and undoped DLC films have been investigated using a range of surface analysis techniques using Raman spectroscopy and atomic force microscopy (AFM). Raman spectra of doped DLC show that silicon doped DLC reduces the growth range of the ID/IG ratio, with a significant red-shift of the G peak position. Following exposure to protein, for undoped DLC the peaks at 1664 cm−1 and around 1241 cm−1 can be attributed to amide I and III, respectively, with an increase in the surface morphology of the surfaces giving some indication of the protein structure on the surfaces. Results indicate that HSA exhibit the majority of β-sheet during the adsorption on the surfaces. The results showed that the silicon incorporation DLC tends to increase of surface roughness and the adsorbed level of HSA is higher with higher levels of silicon doping of the DLC. Therefore, doping DLC may provide a method of controlling the adsorption of protein

A systematically coarse-grained model for DNA, and its predictions for persistence length, stacking, twist, and chirality

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain, for both single- and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.Comment: 30 pages, 20 figures, Supplementary Material available at http://www.physics.ubc.ca/~steve/publications.htm