| 1. |
- Lee, K., et al.
(författare)
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Higher-accuracy van der Waals density functional
- 2010
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Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 82:8
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Tidskriftsartikel (refereegranskat)abstract
- We propose a second version of the van der Waals density functional of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)], employing a more accurate semilocal exchange functional and the use of a large-N asymptote gradient correction in determining the vdW kernel. The predicted binding energy, equilibrium separation, and potential-energy curve shape are close to those of accurate quantum chemical calculations on 22 duplexes. We anticipate the enabling of chemically accurate calculations in sparse materials of importance for condensed matter, surface, chemical, and biological physics.
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| 2. |
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| 3. |
- Cooper, V.R., et al.
(författare)
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Stacking Interactions and the Twist of DNA
- 2008
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Ingår i: Journal of the American Chemical Society. ; 130, s. 1304-
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Tidskriftsartikel (refereegranskat)abstract
- The importance of stacking interactions for the Twist and stability of DNA is investigated using the fully ab initio van der Waals density functional (vdW-DF). Our results highlight the role that binary interactions between adjacent sets of base pairs play in defining the sequence-dependent Twists observed in high-resolution experiments. Furthermore, they demonstrate that additional stability gained by the presence of thymine is due to methyl interactions with neighboring bases, thus adding to our understanding of the mechanisms that contribute to the relative stability of DNA and RNA. Our mapping of the energy required to twist each of the 10 unique base pair steps should provide valuable information for future studies of nucleic acid stability and dynamics. The method introduced will enable the nonempirical theoretical study of significantly larger pieces of DNA or DNA/amino acid complexes than previously possible.
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| 4. |
- Langreth, D. C., et al.
(författare)
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A density functional for sparse matter
- 2009
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Ingår i: Journal of Physics Condensed Matter. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 21:8, s. 084203-
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Tidskriftsartikel (refereegranskat)abstract
- Sparse matter is abundant and has both strong local bonds and weak nonbonding forces, in particular nonlocal van der Waals (vdW) forces between atoms separated by empty space. It encompasses a broad spectrum of systems, like soft matter, adsorption systems and biostructures. Density-functional theory (DFT), long since proven successful for dense matter, seems now to have come to a point, where useful extensions to sparse matter are available. In particular, a functional form, vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401; Thonhauser et al 2007 Phys. Rev. B 76 125112), has been proposed for the nonlocal correlations between electrons and applied to various relevant molecules and materials, including to those layered systems like graphite, boron nitride and molybdenum sulfide, to dimers of benzene, polycyclic aromatic hydrocarbons (PAHs), doped benzene, cytosine and DNA base pairs, to nonbonding forces in molecules, to adsorbed molecules, like benzene, naphthalene, phenol and adenine on graphite, alumina and metals, to polymer and carbon nanotube (CNT) crystals, and hydrogen storage in graphite and metal–organic frameworks (MOFs), and to the structure of DNA and of DNA with intercalators. Comparison with results from wavefunction calculations for the smaller systems and with experimental data for the extended ones show the vdW-DF path to be promising. This could have great ramifications.
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| 5. |
- Langreth, D. C., et al.
(författare)
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Comment on "Nonlocal Van Der Waals Density Functional Made Simple”
- 2010
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 104:9
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Tidskriftsartikel (refereegranskat)abstract
- A Comment on the Letter by Oleg A. Vydrov and Troy Van Voorhis, Phys. Rev. Lett.PRLTAO0031-9007 103, 063004 (2009)10.1103/PhysRevLett.103.063004. The authors of the Letter offer a Reply.
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| 6. |
- Langreth, D. C., et al.
(författare)
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Van der Waals Density Functional Theory with Applications
- 2005
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 101:5, s. 599-610
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Tidskriftsartikel (refereegranskat)abstract
- The details of a density functional that includes van der Waals (vdW) interactions are presented. In particular we give some key steps of the transition from a form for fully planar systems to a procedure for realistic layered compounds that have planar symmetry only on large-distance scales, and which have strong covalent bonds within the layers. It is shown that the random-phase approximation of that original functional can be replaced by an approximation that is exact at large separation between vdW interacting fragments and seamless as the fragments merge. An approximation to the latter which renders the functional easily applicable and which preserves useful accuracy in both limits and in between is given. We report additional data from applications to forms of graphite, boron nitride, and molybdenum sulfide not reported in our previous communication.(C) 2004 Wiley Periodicals, Inc.
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| 7. |
- Li, S, et al.
(författare)
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Stacking Interactions and DNA Intercalation
- 2009
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 113:32, s. 11166-
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Tidskriftsartikel (refereegranskat)abstract
- The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair-base-pair interactions and that of the stacked intercalator-base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair-intercalator interactions call provide valuable information for future nonempirical studies of DNA intercalation dynamics.
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