Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties

Riley, Kevin E.; Holt, Bryan T. Op’t; Merz, Kenneth M.

doi:10.1021/ct600185a

Cited by 309 publications

(270 citation statements)

References 112 publications

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“…Autogenerated delocalized coordinates [10] were used in geometry optimizations with a medium-sized basis set, 6-31+G(d), since increasing the basis sets to triple-ζ quality gives very small additional corrections to the geometries while dramatically increasing the computational cost, and the use of such large basis sets for geometry optimization is often considered unnecessary from a computational point of view [11][12][13]. Accurate DFT energies of the optimized geometries obtained with each density functional were then calculated using the same functional with several triple-ζ quality basis sets: 6-311+G(d,p), 6-311+G(2d,p), 6-311+G(2d,2p), and 6-311+G(3d,2p).…”

Section: Methodsmentioning

confidence: 99%

Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest

Silva

Ramos

2011

Computational and Theoretical Chemistry

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Abstract:The performance of 18 different DFT functionals in the prediction of absolute and relative energies of organic and biochemical acid/base and redox reactions was evaluated, using MP2 extrapolated to the complete basis set limit and CCSD(T)/aug-cc-pVTZ energies as benchmark.Absolute reduction energies were predicted with relatively large average errors (2-4 kcal.mol -1 ) except for the best functional, PBE0 (1.3±1.2 kcal.mol -1 ). The DFT predictions of relative reduction energies afforded mean unsigned errors (2.1 kcal.mol -1 for the best functional, PBE0) which, although relatively large, are smaller than those obtained with MP2 with comparable basis sets (3.2 kcal.mol -1 ). This relatively poor performance was mostly due to significant underprediction of the reduction energy of a model disulfide bridge, and overprediction of that of a model quinone, as eliminating these reaction from the test set enables most of the tested hybrid-GGA functionals (B3LYP, B3PW91, B97-1, BHHLYP, PBE0, PBE1PW91, X3LYP), though not meta-GGA or meta-hybrid-GGA functionals, to achieve small mean unsigned errors (<1.5 kcal.mol -1 ). In the acid/base reaction test set, several hybrid-

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Section: Methodsmentioning

confidence: 99%

Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest

Silva

Ramos

2011

Computational and Theoretical Chemistry

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“…DFT calculates the ground state energy of a system as a functional of its electronic density while approximating the exchange and correlation (XC) component of the energy functional. The simplest XC approximation is the time-honoured local density approximation (LDA), which produces significant errors when computing AEAs [121]. The next rung in the ladder is the Generalised Gradient Approximation (GGA), that includes the density and its gradient.…”

Section: Electron Affinitiesmentioning

confidence: 99%

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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Abstract. DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts from the interaction of radiation -either photons or swift ions -with the biological medium. Such interactions cause electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, in particular strand breaks in plasmid DNA [1]. These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage.In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.

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“…All calculations were performed with Gaussian 03 (Gaussian Inc., USA) [23]. The expected uncertainty of this treatment is ϳ10 kcal mol -1 , which is a factor of 1.5-2 lower than that of the AM1 model [24,25].…”

Section: Data Processing For Calibrating Ion Internal Energiesmentioning

confidence: 99%

Fragmentation of benzylpyridinium “thermometer” ions and its effect on the accuracy of internal energy calibration

Barylyuk

Chingin

Balabin

et al. 2010

J. Am. Soc. Mass Spectrom.

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Electrospray ionization mass spectrometry (ESI-MS) is a powerful analytical method to study biomolecules and noncovalent complexes. The prerequisite for their intact observation is soft ionization. In ESI, the internal energy of ions is primarily influenced by collisional activation in the source. The survival yield method is frequently used to probe the energy deposition in ions during the electrospray process. In the present work, we investigate the fragmentation pathways of para-substituted benzylpyridinium ions, the most widely used "thermometer ions" in the survival yield method. In addition to the C-N bond cleavage, alternative fragmentation channels were found for the compounds studied. We consider these pathways to result from intramolecular rearrangements. The effect of these additional fragments on the accuracy of the internal energy calibration is estimated for both collision-cell and in-source collision-induced dissociation (CID). Altogether, results presented suggest that a correction of the energy scale is necessary for the method based on benzylpyridinium ions to precisely quantify ion internal energies. (J Am Soc Mass Spectrom 2010, 21, 172-177) © 2010 American Society for Mass Spectrometry E lectrospray ionization mass spectrometry (ESI-MS) [1] is widely used to characterize various species, from small organic compounds [2] to large supramolecular assemblies of biopolymers [3]. In the ESI source, small charged droplets containing dissolved analyte are produced at atmospheric pressure. As the droplets migrate along a voltage gradient to the low-pressure region of the mass spectrometer, solvent evaporates, releasing unsolvated ions. Ions produced in the ion source undergo collisions with ambient gas molecules and thereby accumulate internal energy. Such collisional activation often results in fragmentation and/or rearrangement of ions [4,5]. The effect is more pronounced for weak interactions, such as those involved in noncovalent complexes, which are widely studied by ESI-MS [5]. In addition, for instruments with restricted MS/MS capabilities, so-called in-source CID is frequently the only way to obtain structural information on the parent ions. In-source CID strongly depends on instrument parameter settings and experimental conditions, thus resulting in poor reproducibility of the MS/MS spectra [5]. Internal energy deposition in ions generally affects the mass spectra. It is therefore important to control the ion internal energy for many applications, such as optimizing the molecular ion abundance, structure determination, differentiation of isomers, MS n experiments, and in the study of non-ovalent complexes [5].The survival yield method was introduced to calibrate the internal energy distribution of ions after collisional activation [6,7]. In this method, compounds with a simple and well known dissociation pattern, so-called thermometer ions, are used to probe the energy uptake due to the activation process. The survival yield is the ratio of the parent ion intensity to the sum of parent and f...

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Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties

Cited by 309 publications

References 112 publications

Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest

Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Fragmentation of benzylpyridinium “thermometer” ions and its effect on the accuracy of internal energy calibration

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