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- Berland, Kristian, 1983, et al.
(author)
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A van der Waals density functional study of adenine on graphene: Single-molecular adsorption and overlayer binding
- 2011
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In: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 23, s. 135001-
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Journal article (peer-reviewed)abstract
- The adsorption of an adenine molecule on graphene is studied using a first-principles van der Waals functional, vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401). The cohesive energy of an ordered adenine overlayer is also estimated. For the adsorption of a single molecule, we determine the optimal binding configuration and adsorption energy by translating and rotating the molecule. The adsorption energy for a single molecule of adenine is found to be 711 meV, which is close to the calculated adsorption energy of the similarly sized naphthalene. On the basis of the single-molecular binding configuration, we estimate the cohesive energy of a two-dimensional ordered overlayer. We find a significantly stronger binding energy for the ordered overlayer than for single-molecule adsorption.
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- Chakarova Käck, Svetla, 1977, et al.
(author)
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Binding of polycyclic aromatic hydrocarbons and graphene dimers in density functional theory
- 2010
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In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 12, s. Art. Nr. 013017-
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Journal article (peer-reviewed)abstract
- An early van der Waals density functional (vdW-DF) described layered systems (such as graphite and graphene dimers) using a layer-averaged electron density in the evaluation of nonlocal correlations. This early vdW-DF version was also adapted to approximate the binding of polycyclic aromatic hydrocarbons (PAHs) (Chakarova S D and Schröder E 2005 J. Chem. Phys. 122 054102). In parallel to that PAH study, a new vdW-DF version (Dion M, Rydberg H, Schröder E, Langreth D C and Lundqvist B I 2004 Phys. Rev. Lett. 92 246401) was developed that provides accounts of nonlocal correlations for systems of general geometry. We apply here the latter vdW-DF version to aromatic dimers of benzene, naphthalene, anthracene and pyrene, stacked in sandwich (AA) structure, and the slipped-parallel (AB) naphthalene dimer. We further compare the results of the two methods as well as other theoretical results obtained by quantum-chemistry methods. We also compare calculations for two interacting graphene sheets in the AA and the AB structures and provide the corresponding graphene-from-graphite exfoliation energies. Finally, we present an overview of the scaling of the molecular–dimer interaction with the number of carbon atoms and with the number of carbon rings.
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- Chakarova Käck, Svetla, 1977
(author)
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Protein unfolding by interfaces and interactions between polycyclic aromatic hydrocarbons
- 2004
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Licentiate thesis (other academic/artistic)abstract
- In order to theoretically study large and complex systems, a variety of approaches that can be categorized loosely as top-down or bottom-up are followed. While our vision is to bridge the gap between these approaches and use them together in multiscale materials modeling, the present thesis is limited to give examples of each type of approach in the study of soft-matter systems.In the first part of the thesis, a top-down approach to the study of interface-induced protein unfolding on hydrophobic and polar interfaces, respectively, is presented. We use a two-dimensional lattice model and an exhaustive enumeration search for the ground state structures for a set of model proteins of length 20 residues. A comparative model study of the effects of the two types of interfaces show them to induce similar behaviour, however, with stronger effectsfor hydrophobic interfaces. The unfolding is found to proceed by a large and sudden loss of native contacts. Further, the resistance of proteins to unfolding on hydrophobic interfaces is in our model positively correlated with (i) the magnitude of the folding energy in the native-state structure, (ii) the thermal stability or energy gap for that structure, and (iii) the interface energy for native-state adsorption. We find these factors to be of roughly equal importance. Finally, experiments that might test the predicted correlations are proposed.The second part of the thesis presents a bottom-up approach, a first-principles calculation on dimers of polycyclic aromatic hydrocarbon (PAH) molecules. In sparse matter, to which these and also proteins belong,the van der Waals forces, which are weak but long-ranged, have important effects. The PAHs consist of aromatic rings, molecularunits that also appear in the side chains of amino acids. A recently developed van der Waals density functional [Phys.Rev.Lett. 91, 126402 (2003)] for planar geometry is used in an otherwise standard implementation of thedensity functional theory to calculate the van der Waalsinteractions between the PAH molecules. Calculated values for binding distances and energies of dimers of benzene, naphthalene, anthracene and pyrene are consistent with those of experiments and other theoretical studies.This pilot study gives promise for deepened investigations of interactions of proteins, mutually and at interfaces.
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- Chakarova Käck, Svetla, 1977
(author)
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Towards First-Principles Understanding of Biomolecular Adsorption
- 2006
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Doctoral thesis (other academic/artistic)abstract
- A fundamental understanding of the interactions of biomolecules, such as proteins and DNA, with surfaces is of immense importance in numerous applications and poses a true challenge for theory. Density functional theory (DFT) is a quantum-mechanical tool well established for its ability to balance large system size with good accuracy in first-principles studies. However, traditional implementations cannot describe the nonlocal van der Waals interactions, that are essential in many soft matter systems, including biomolecule-surface interactions. Recently, a van der Waals density functional (vdW-DF) has been developed, making DFT applicable to soft matter. Since the functional is new, it is important to evaluate its performance. Here two versions of vdW-DF are applied to study dimers of benzene, naphthalene, anthracene and pyrene (molecules from the polycyclic aromatic hydrocarbon (PAH) family), as well as to interacting graphite sheets.Further, we consider several key systems of molecular adsorption, in particular, adsorption of benzene, naphthalene, phenol, and adenine on a graphite surface.These systems have aromatic rings, molecular units that also appear in the side chains of amino acids in proteins, and are also important in DNA interactions, where adenine is one of the four DNA base-pairs. They are ideal models for van der Waals bonded complexes and thus very suitable for vdW-DF performance tests. We calculate values for binding distances and energies andfind these consistent with those of experiments and other theoretical studies using accurate wave-function based methods. However, the latter methods find even our small-dimer systems laborious, the larger dimers nearly impossible to treat, and cannot treat molecular adsorption, in which respect vdW-DF is more or less unique.Based on the comparison with experimental data, our results show great promise for broad application of the vdW-DF to soft matter systems.Simulation of a system with size close to that of complex biomolecules, such as proteins, requires a multi-scale approach. We present a model study of protein unfolding upon adsorption that applies a simple but exactly solvable two-dimensional lattice model, describing amino acids based on their hydrophobicities. This approach indicatesthe effect of hydrophobic and polar surfaces, as well as the factors influencing protein stability, and we propose experiments to test the predicted correlations.In summary, we treat biomolecule-surface interactions on two scales. The prospect of obtaining a deeper insight by bridging them to a complete description is judged very promising, given our steps taken towards a first-principles understanding of biomolecular adsorption.
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