Trapping of electrons near chemisorbed hydrogen on graphene

Chemical adsorption of atomic hydrogen on a negatively charged single layer graphene sheet has been analyzed with ab-initio Density Functional Theory calculations. We have simulated both finite clusters and infinite periodic systems to investigate the effect of different ingredients of the theory, e.g. exchange and correlation potentials, basis sets, etc. Hydrogen's electron affinity dominates the energetic balance in the charged systems and the extra electron is predominantly attracted to a region nearby the chemisorbed atom. The main consequences are: (i) the cancellation of the unpaired spin resulting in a singlet ground-state, and (ii) a stronger interaction between hydrogen and the graphene sheet.Comment: 11 pages, 8 figures, to be published in PR

Grid-based density functional calculation of many-electron systems

Exploratory variational pseudopotential density functional calculations are performed for the electronic properties of many-electron systems in the 3D cartesian coordinate grid (CCG). The atom-centered localized gaussian basis set, electronic density and the two-body potentials are set up in the 3D cubic box. The classical Hartree potential is calculated accurately and efficiently through a Fourier convolution technique. As a first step, simple local density functionals of homogeneous electron gas are used for the exchange-correlation potential, while Hay-Wadt-type effective core potentials are employed to eliminate the core electrons. No auxiliary basis set is invoked. Preliminary illustrative calculations on total energies, individual energy components, eigenvalues, potential energy curves, ionization energies, atomization energies of a set of 12 molecules show excellent agreement with the corresponding reference values of atom-centered grid as well as the grid-free calculation. Results for 3 atoms are also given. Combination of CCG and the convolution procedure used for classical Coulomb potential can provide reasonably accurate and reliable results for many-electron systems.Comment: 17 pages, 1 figure, 6 tables, 34 reference

Are hemispherical caps of boron-nitride nanotubes possible?

We report all-electron, density-functional calculations with large Gaussian polarization basis set of the recently synthesized octahedral B24N24 cage that is perfectly round by symmetry, and boron-nitride (BN) clusters that its existence might suggest. We consider whether it is energetically possible that the two halves of this round cage could cap the BN nanotubes, modeled by B28N28 and B32N32. The energetics show that BN nanotubes with such round caps, are only slightly less favorable than the BN clusters containing six squares as the only defects in the otherwise perfect hexagonal lattice. A larger B96N96 octahedral cage formed from B24N24 by adding sufficient hexagons to isolate all squares is not very favorable energetically. The squares protrude noticeably from its otherwise round surface.Comment: Uses elsart.cls (Elsevier Science), (Better pictures can be obtained from authors); Manuscript to appear in Chemical Physics Letter

Magnetic molecules created by hydrogenation of Polycyclic Aromatic Hydrocarbons

Present routes to produce magnetic organic-based materials adopt a common strategy: the use of magnetic species (atoms, polyradicals, etc.) as building blocks. We explore an alternative approach which consists of selective hydrogenation of Polycyclic Aromatic Hydrocarbons. Self-Consistent-Field (SCF) (Hartree-Fock and DFT) and multi-configurational (CISD and MCSCF) calculations on coronene and corannulene, both hexa-hydrogenated, show that the formation of stable high spin species is possible. The spin of the ground states is discussed in terms of the Hund rule and Lieb's theorem for bipartite lattices (alternant hydrocarbons in this case). This proposal opens a new door to magnetism in the organic world.Comment: 6 pages, 4 figures and 2 table

Mechanical and Structural Characterization of Semicrystalline Polyethylene under Tensile Deformation by Molecular Dynamics Simulations

We have studied tensile deformations of semicrystalline polyethylene (PE) with molecular dynamics simulations at two different strain rates and temperatures. Compared to earlier studies, the modeled systems were approximately 5 times larger, which allowed significantly larger strains up to about 120% to be examined. Two different modes of structural transformation of semicrystalline PE were observed at the higher temperature of 350 K, depending on the strain rate. At the faster strain rate of 5 × 10⁷ s⁻¹, cavitation in the noncrystalline region dominated, with little change in the crystalline region, resulting in monotonically declining stress with increasing strain after the yield point. However, in a small number of cases, significant deviations from the average stress–strain profile were observed that correlated with topological constraints, such as bridges and bridging entanglements connecting crystalline regions separated by the noncrystalline region, and destabilization of the crystalline region. At the slower strain rate of 5 × 10⁶ s⁻¹, we observed repeated melting/recrystallization events and significant oscillations in stress associated with variations of density in crystalline and noncrystalline regions and the displacement of polymer chains from crystalline to noncrystalline regions. When averaged over an ensemble of starting configurations for semicrystalline PE, the oscillations were found to be less coherent from microstate to microstate and offset one another. The postyield stress became notably smoother and began to resemble the plastic flow observed macroscopically, followed by stress hardening at the later stage of deformation. At the lower temperature of 250 K, cavity formation was the only mechanism observed, for both strain rates. The interplay between the thermodynamic stability of the crystalline region and the topological constraints imposed by bridges and entanglements in the noncrystalline region is crucial to understanding structural transformations of semicrystalline PE during tensile deformations.U.S. Army Research Laborator

Functional and genomic analysis of MEF2 transcription factors in neural development

Development of the central nervous system requires the precise coordination of intrinsic genetic programs to instruct cell fate, synaptic connectivity and function. The MEF2 family of transcription factors (TFs) plays many essential roles in neural development; however, the mechanisms of gene regulation by MEF2 in neurons remain unclear. This dissertation focuses on the molecular mechanisms by which MEF2 binds to the genome, activates enhancers, and regulates gene expression within the developing nervous system. We find that one MEF2 family member in particular, MEF2D, is an essential regulator of the development and function of retinal photoreceptors, the primary sensory neurons responsible for vision. Despite being expressed broadly across many tissues, in the retina MEF2D binds to retina-specific enhancers and regulates photoreceptor-specific transcripts, including critical retinal disease genes. Functional genome-wide analyses demonstrate that MEF2D achieves tissue-specific binding and action through cooperation with a retina-specific TF, CRX. CRX recruits MEF2D away from canonical MEF2 binding sites by promoting MEF2D binding to retina-specific enhancers that lack a strong consensus MEF2 binding sequence. MEF2D and CRX then synergistically co-activate these enhancers to regulate a cohort of genes critical for normal photoreceptor development. These findings demonstrate that MEF2D, a broadly expressed TF, contributes to retina-specific gene expression in photoreceptor development by binding to and activating tissue-specific enhancers cooperatively with CRX, a tissue-specific co-factor. A major unresolved feature of MEF2D function in the retina is that the number of MEF2D binding sites significantly exceeds the number of genes that are dependent on MEF2D for expression. We investigated causes of this discrepancy in an unbiased manner by characterizing the activity of MEF2D-bound enhancers genome-wide. We find that many MEF2D-bound enhancers are inactive. Furthermore, less than half of active MEF2D-bound enhancers require MEF2D for activity, suggesting that significant redundancies exist for TF function within enhancers. These findings demonstrate that observed TF binding significantly overestimates direct TF regulation of gene expression. Taken together, our results suggest that the broadly expressed TF MEF2D achieves tissue specificity through competitive recruitment to enhancers by tissue-specific TFs and activates a small subset of enhancers to regulate genes

A Theoretical Study of the Reaction of Ti+ with Ethane

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H+4+H2 and Ti++C2H6→TiCH+2+CH4reactions are studied using density functional theory(DFT) with the B3LYP functional and ab initiocoupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory