Adiabatic Connection for Kinetics

The central quantity of density functional theory is the so-called exchange-correlation functional. This quantity encompasses all non-trivial many-body effects of the ground-state and has to be approximated in any practical application of the theory. For the past 50 years, hundreds of such approximations have appeared, with many successfully persisting in the electronic structure community and literature. Here, we present a library that contains routines to evaluate many of these functionals (around 180) and their derivatives.

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“…As one can see, the typical execution time within Libxc is much smaller than the total time required in the whole calculation. [165] …”

Section: Appendix A: Available Functionalsmentioning

confidence: 99%

Libxc: A library of exchange and correlation functionals for density functional theory

Marques¹,

Oliveira²,

Burnus³

2012

Computer Physics Communications

481

375

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“…The MPW1K/6−31+G * * [101] barrier for proton transfer from the C2 atom of sugar to C6 of (Cy+H) − is 5.6, 3.4, and 4.2 kcal/mol in terms of electronic energy, electronic energy corrected for zero-point vibrations, and Gibbs free energy, respectively (the MPW1K functional was specifically designed to reproduce barrier heights of chemical reactions). The proton transfer leads formally to a product, in which the negative charge is localized on the sugar unit.…”

Section: Two-electron Mechanisms Of Dna Damage Triggered By Excess Elmentioning

confidence: 99%

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

Rak

Mazurkiewicz

Kobyłecka

et al. 2008

Challenges and Advances in Computational Chemistry and Physics

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Abstract:The last decade has witnessed immense advances in our understanding of the effects of ionizing radiation on biological systems. As the genetic information carrier in biological systems, DNA is the most important species which is prone to damage by high energy photons. Ionizing radiations destroy DNA indirectly by forming low energy electrons (LEEs) as secondary products of the interaction between ionizing radiation and water. An understanding of the mechanism that leads to the formation of single and double strand breaks may be important in guiding the further development of anticancer radiation therapy. In this article we demonstrate the likely involvement of stable nucleobases anions in the formation of DNA strand breaks -a concept which the radiation research community has not focused on so far. In Section 21.1 we discuss the current status of studies related to the interaction between DNA and LEEs. The next section is devoted to the description of proton transfer induced by electron attachment to the complexes between nucleobases and various proton donorsa process leading to the strong stabilization of nucleobases anions. Then, we review our results concerning the anionic binary complexes of nucleobases with particular emphasize on the GC and AT systems. Next, the possible consequences of interactions between DNA and proteins in the context of electron attachment are briefly discussed. Further, we focus on existing proposal of single strand break formation in DNA. Ultimately, open questions as well perspectives of studies on electron induced DNA damage are discussed

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“…An increase in the exact Hartree-Fock exchange from 0% in pure DFT to 20% in B3LYP to 50% in BHLYP leads to better error cancellation between the reactants and transition states for the computation of barrier heights. 80,82,83 Using restricted orbitals causes most of the DFT barrier heights ∆E ‡ to increase. This significantly improves results for the reaction of H 2 with H, but for the other two symmetric reactions the RBHLYP barriers are overestimated compared to RCCSD(T).…”

Section: Symmetric Reactionsmentioning

confidence: 99%

High-Level ab Initio Studies of Hydrogen Abstraction from Prototype Hydrocarbon Systems

et al. 2006

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Symmetric and non-symmetric hydrogen abstraction reactions are studied using stateof-the-art ab initio electronic structure methods. Second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles, doubles and perturbative triples [CCSD(T)] methods with large correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used in determining the transition-state geometries, activation barriers, and thermodynamic properties of several representative hydrogen abstraction reactions. The importance of basis set, electron correlation, and choice of zeroth-order reference wavefunction in the accurate prediction of activation barriers and reaction enthalpies are also investigated. The ethynyl radical (·CCH), which has a very high affinity for hydrogen atoms, is studied as a prototype hydrogen abstraction agent. Our high-level quantum mechanical computations indicate that hydrogen abstraction using the ethynyl radical has an activation energy of less than 3 kcal mol −1 for * To whom correspondence should be addressed. E-mail addresses: sherrill@gatech.edu; merkle@cc.gatech.edu; rfreitas@rfreitas.com 1 hydrogens bonded to an sp 2 or sp 3 carbon. These low activation barriers further corroborate previous studies suggesting that ethynyl-type radicals would make good tooltips for abstracting hydrogens from diamondoid surfaces during mechanosynthesis. Modeling the diamond C(111) surface with isobutane and treating the ethynyl radical as a tooltip, hydrogen abstraction in this reaction is predicted to be barrierless.

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Adiabatic Connection for Kinetics

Cited by 1,470 publications

References 49 publications

Libxc: A library of exchange and correlation functionals for density functional theory

Libxc: A library of exchange and correlation functionals for density functional theory

Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons

High-Level ab Initio Studies of Hydrogen Abstraction from Prototype Hydrocarbon Systems

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